ZNF260

Summary

ZNF260 (zinc finger protein 260, HGNC:13499) is a protein-coding gene on chromosome 19q13.12, encoding Zinc finger protein 260 (Q3ZCT1). Transcription factor that acts as a cardiac regulator and an effector of alpha1-adrenergic signaling.

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. Located in cytosol and nucleoplasm.

Source: NCBI Gene 339324 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_001166037

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13499
Approved symbol	ZNF260
Name	zinc finger protein 260
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	ozrf1, Zfp260
Ensembl gene	ENSG00000254004
Ensembl biotype	protein_coding
OMIM	613749
Entrez	339324

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 16 protein_coding, 1 retained_intron

ENST00000520608, ENST00000523638, ENST00000588993, ENST00000592282, ENST00000593142, ENST00000855526, ENST00000855527, ENST00000855528, ENST00000927402, ENST00000927403, ENST00000927404, ENST00000927405, ENST00000927406, ENST00000927407, ENST00000927408, ENST00000927409, ENST00000952161

RefSeq mRNA: 7 — MANE Select: NM_001166037 NM_001012756, NM_001166036, NM_001166037, NM_001166038, NM_001375596, NM_001375597, NM_001375598

CCDS: CCDS33003

Canonical transcript exons

ENST00000523638 — 3 exons

Exon	Start	End
ENSE00002091524	36528219	36528271
ENSE00002123530	36510687	36515699
ENSE00002295470	36525155	36525373

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 91.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.0679 / max 182.1816, expressed in 1688 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180680	8.1930	1646
180681	0.8749	509

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	91.69	gold quality
endothelial cell	CL:0000115	91.49	gold quality
amniotic fluid	UBERON:0000173	91.23	gold quality
pancreatic ductal cell	CL:0002079	91.11	gold quality
epithelial cell of pancreas	CL:0000083	90.96	gold quality
visceral pleura	UBERON:0002401	88.57	gold quality
ganglionic eminence	UBERON:0004023	88.38	gold quality
palpebral conjunctiva	UBERON:0001812	87.81	gold quality
parietal pleura	UBERON:0002400	87.50	gold quality
ileal mucosa	UBERON:0000331	87.34	gold quality
adrenal tissue	UBERON:0018303	87.08	gold quality
ventricular zone	UBERON:0003053	87.03	gold quality
pigmented layer of retina	UBERON:0001782	86.78	gold quality
kidney epithelium	UBERON:0004819	86.08	silver quality
cortical plate	UBERON:0005343	85.96	gold quality
endometrium	UBERON:0001295	85.78	gold quality
germinal epithelium of ovary	UBERON:0001304	85.55	gold quality
thymus	UBERON:0002370	84.67	gold quality
calcaneal tendon	UBERON:0003701	84.16	gold quality
tibialis anterior	UBERON:0001385	83.97	silver quality
mucosa of paranasal sinus	UBERON:0005030	83.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.71	gold quality
esophagus squamous epithelium	UBERON:0006920	83.69	gold quality
tibia	UBERON:0000979	83.39	gold quality
islet of Langerhans	UBERON:0000006	83.29	gold quality
corpus callosum	UBERON:0002336	83.26	gold quality
medial globus pallidus	UBERON:0002477	83.21	gold quality
epithelium of mammary gland	UBERON:0003244	82.83	gold quality
mammary duct	UBERON:0001765	82.74	gold quality
middle temporal gyrus	UBERON:0002771	82.32	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	11.38
E-ANND-3	yes	4.44

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
ADRA1D
GATA4	Activation
NPPA	Activation

JASPAR motifs

Motif	Name	Family
MA2457.1	ZNF260	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

147 targeting ZNF260, 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-656-3P	100.00	72.15	2788
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
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-144-3P	99.94	73.98	2698
HSA-MIR-101-3P	99.94	75.03	2230

Literature-anchored findings (GeneRIF, showing 1)

• Zfp260 is a novel transcriptional regulator in normal and pathological heart development and a nuclear effector of alpha1-adrenergic signaling (PMID:16166646)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp260	ENSMUSG00000049421
rattus_norvegicus	Zfp260	ENSRNOG00000020762

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 260 — Q3ZCT1 (reviewed: Q3ZCT1)

All UniProt accessions (1): Q3ZCT1

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that acts as a cardiac regulator and an effector of alpha1-adrenergic signaling. Binds to PE response elements (PERE) present in the promoter of genes such as ANF/NPPA and acts as a direct transcriptional activator of NPPA. Also acts as a cofactor with GATA4, a key cardiac regulator.

Subunit / interactions. Binds DNA. Interacts with GATA4.

Subcellular location. Nucleus.

Induction. Up-regulated by activation of alpha1-adrenergic receptors.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (7): NP_001012774, NP_001159508, NP_001159509, NP_001159510, NP_001362525, NP_001362526, NP_001362527 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF13465

UniProt features (14 total): zinc finger region 13, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3ZCT1-F1	82.02	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): MARTINEZ_RB1_TARGETS_UP, MARSON_FOXP3_TARGETS_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MARTINEZ_RB1_AND_TP53_TARGETS_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP, KYNG_NORMAL_AGING_UP, KYNG_WERNER_SYNDROM_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, LI_INDUCED_T_TO_NATURAL_KILLER_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CDC5L_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): 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), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cellular anatomical structure	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF260	GATA4	P43694	586
ZNF260	NPPA	P01160	554
ZNF260	EDN1	P05305	527
ZNF260	ZNF738	Q8NE65	373
ZNF260	WFDC10B	Q8IUB3	370
ZNF260	TRIM74	Q86UV6	366
ZNF260	PHF3	Q92576	365
ZNF260	CYP4Z1	Q86W10	348
ZNF260	ZNG1F	Q4V339	348
ZNF260	ZNG1E	Q5RIA9	348
ZNF260	ZNG1C	Q5JTY5	339
ZNF260	BLTP1	Q2LD37	332
ZNF260	K7EJK4	K7EJK4	324
ZNF260	TMEM263	Q8WUH6	323
ZNF260	INSYN2A	Q6ZSG2	322

IntAct

20 interactions, top by confidence:

A	B	Type	Score
ZNF260	NDEL1	psi-mi:“MI:0915”(physical association)	0.560
NDEL1	ZNF260	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF260	psi-mi:“MI:0915”(physical association)	0.560
ZNF260	ZNF648	psi-mi:“MI:0915”(physical association)	0.560
EN1	NFIB	psi-mi:“MI:2364”(proximity)	0.470
NELL1	MATN2	psi-mi:“MI:0914”(association)	0.350
DDR2	PLD2	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
GCM1	BCL9	psi-mi:“MI:2364”(proximity)	0.270
NHLH1	IGF2BP3	psi-mi:“MI:2364”(proximity)	0.270
HNF1B	BCL9	psi-mi:“MI:2364”(proximity)	0.270
TLX1	BCL9	psi-mi:“MI:2364”(proximity)	0.270
ZNF260	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.000
ZNF648	ZNF260	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): ZNF260 (Two-hybrid), ZNF260 (Synthetic Lethality), ZNF260 (Affinity Capture-MS), ZNF260 (Affinity Capture-MS), ZNF260 (Two-hybrid), KRTAP10-7 (Two-hybrid), ZNF260 (Affinity Capture-MS), ZNF260 (Affinity Capture-MS), ZNF260 (Affinity Capture-MS), ZNF260 (Proximity Label-MS), ZNF260 (Proximity Label-MS), ZNF260 (Proximity Label-MS), ZNF260 (Proximity Label-MS), ZNF260 (Proximity Label-MS), ZNF260 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDQ7, A6NK75, A6NNF4, A8MQ14, A8MTY0, C9JN71, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17019, P17039, P35789, P51522, Q03923, Q03938, Q08AN1, Q14585, Q3SYV7, Q3ZCT1, Q4R4C7, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5RDX1, Q5SXM1, Q6P5C7, Q6ZN08, Q6ZN57, Q6ZR52, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N972

Diamond homologs: Q3ZCT1, Q62513, Q62981, P18741

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

641 predictions. Top by Δscore:

Variant	Effect	Δscore
19:36528215:TCAC:T	donor_loss	0.9900
19:36528216:CACCG:C	donor_loss	0.9900
19:36528217:A:AC	donor_gain	0.9900
19:36528217:ACC:A	donor_loss	0.9900
19:36528217:ACCGG:A	donor_gain	0.9900
19:36528218:C:CC	donor_gain	0.9900
19:36528218:C:G	donor_loss	0.9900
19:36528218:CCGG:C	donor_gain	0.9900
19:36528218:CCGGC:C	donor_gain	0.9900
19:36515700:C:CC	acceptor_gain	0.9800
19:36528213:A:C	donor_gain	0.9800
19:36528217:AC:A	donor_gain	0.9800
19:36528218:CC:C	donor_gain	0.9800
19:36528218:CCG:C	donor_gain	0.9800
19:36515644:A:C	donor_gain	0.9700
19:36515710:G:GC	acceptor_gain	0.9600
19:36515649:CAAGT:C	donor_gain	0.9500
19:36528233:G:GT	donor_gain	0.9500
19:36518707:C:A	donor_gain	0.9100
19:36518740:G:C	donor_gain	0.9100
19:36525914:A:AT	donor_gain	0.9100
19:36515710:G:C	acceptor_gain	0.9000
19:36525168:A:AC	donor_gain	0.8900
19:36525169:C:CC	donor_gain	0.8900
19:36515697:CTT:C	acceptor_gain	0.8800
19:36525193:CATTT:C	donor_gain	0.8700
19:36525238:TTAA:T	donor_gain	0.8700
19:36525194:A:C	donor_gain	0.8600
19:36525913:C:CT	donor_gain	0.8500
19:36525173:CA:C	donor_gain	0.8400

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000190244 (19:36511036 C>A,T), RS1000217599 (19:36512048 T>C), RS1000444566 (19:36517310 G>A), RS1000499667 (19:36511009 CAGA>C), RS1000889015 (19:36522558 T>C), RS1001091448 (19:36528284 G>A,T), RS1001101011 (19:36517447 T>C), RS1001499188 (19:36529768 A>C), RS1001686059 (19:36524630 G>A), RS1001724193 (19:36527085 T>C), RS1001877973 (19:36516740 T>A,C), RS1001888847 (19:36521102 A>C,G), RS1001945895 (19:36518078 C>T), RS1001983939 (19:36521485 G>A), RS1002018300 (19:36523434 T>C)

Disease associations

OMIM: gene MIM:613749 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003074_21	Cerebral amyloid deposition in APOEe4 non-carriers (PET imaging)	8.000000e-07
GCST008058_223	Estimated glomerular filtration rate	4.000000e-12
GCST008059_192	Estimated glomerular filtration rate	8.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007707	cerebral amyloid deposition measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, affects cotreatment, decreases expression	5
sodium arsenite	decreases expression, increases expression	3
Air Pollutants	affects expression, increases abundance, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
beta-methylcholine	affects expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Coumestrol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Asbestos, Crocidolite	increases methylation	1
Sodium Selenite	increases expression	1
Particulate Matter	increases abundance, decreases expression	1
Magnetite Nanoparticles	increases methylation	1

Clinical trials (associated diseases)

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