ZNF560

gene
On this page

Also known as FLJ31986

Summary

ZNF560 (zinc finger protein 560, HGNC:26484) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 560 (Q96MR9). 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 147741 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 134 total
  • MANE Select transcript: NM_152476

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26484
Approved symbolZNF560
Namezinc finger protein 560
Location19p13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ31986
Ensembl geneENSG00000198028
Ensembl biotypeprotein_coding
Entrez147741

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000301480, ENST00000585974

RefSeq mRNA: 2 — MANE Select: NM_152476 NM_001351678, NM_152476

CCDS: CCDS12214

Canonical transcript exons

ENST00000301480 — 10 exons

ExonStartEnd
ENSE0000111706194703929470518
ENSE0000111706394741999474325
ENSE0000111706894696309469710
ENSE0000111707194712969471378
ENSE0000113648494981289498215
ENSE0000113649094985389498616
ENSE0000113650294752849475369
ENSE0000141295694663559468334
ENSE0000178037394731799473259
ENSE0000365018694691059469187

Expression profiles

Bgee: expression breadth broad, 47 present calls, max score 83.14.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6844 / max 51.5336, expressed in 241 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1790060.5756223
1790050.108847

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.14gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099177.98gold quality
right testisUBERON:000453475.37gold quality
left testisUBERON:000453374.25gold quality
testisUBERON:000047372.33gold quality
stromal cell of endometriumCL:000225568.20gold quality
secondary oocyteCL:000065561.19silver quality
cortical plateUBERON:000534356.48gold quality
ventricular zoneUBERON:000305356.12gold quality
ganglionic eminenceUBERON:000402355.96gold quality
placentaUBERON:000198745.91gold quality
oocyteCL:000002343.93gold quality
lower esophagus mucosaUBERON:003583443.55silver quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
granulocyteCL:000009442.89silver quality
vastus lateralisUBERON:000137941.41gold quality
quadriceps femorisUBERON:000137741.37gold quality
superficial temporal arteryUBERON:000161441.33gold quality
palpebral conjunctivaUBERON:000181241.10gold quality
mucosa of paranasal sinusUBERON:000503040.98gold quality
amniotic fluidUBERON:000017340.69gold quality
jejunal mucosaUBERON:000039940.59gold quality
biceps brachiiUBERON:000150740.57gold quality
epithelium of nasopharynxUBERON:000195140.45gold quality
myocardiumUBERON:000234940.45gold quality
gingival epitheliumUBERON:000194940.43gold quality
germinal epithelium of ovaryUBERON:000130440.33gold quality
esophagus squamous epitheliumUBERON:000692040.29gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450240.27gold quality
jejunumUBERON:000211540.18gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting ZNF560, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-493-5P99.9672.472382
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-430299.8967.941187
HSA-MIR-139-5P99.8069.501399
HSA-MIR-425599.7267.701541
HSA-MIR-368599.6268.831621
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-391599.4568.491905
HSA-MIR-4666A-5P99.4169.721887
HSA-MIR-125399.1267.081688
HSA-MIR-519A-2-5P98.7871.741401
HSA-MIR-520B-5P98.7871.741401
HSA-MIR-4684-5P98.2967.991650
HSA-MIR-1211697.9468.91595

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusZfp78ENSMUSG00000055150
rattus_norvegicusENSRNOG00000083797
drosophila_melanogasterCG2712FBGN0024975
drosophila_melanogasterPhsFBGN0036522
drosophila_melanogasterCG3281FBGN0260741

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), ZNF25 (ENSG00000175395), 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)

Protein

Protein identifiers

Zinc finger protein 560Q96MR9 (reviewed: Q96MR9)

All UniProt accessions (1): Q96MR9

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.

RefSeq proteins (2): NP_001338607, NP_689689* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050589Ikaros_C2H2-ZFFamily

Pfam: PF00096, PF01352, PF13912

UniProt features (21 total): zinc finger region 15, domain 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96MR9-F164.240.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 36 (showing top): GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_2_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, FIGUEROA_AML_METHYLATION_CLUSTER_7_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, RATTENBACHER_BOUND_BY_CELF1, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR493_5P, GSE14308_TH1_VS_TH17_DN

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), 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), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

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

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription cis-regulatory region binding1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
transition metal ion binding1
nucleic acid binding1
DNA binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

310 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF560HMX2A2RU54380
ZNF560LRRIQ3A6PVS8349
ZNF560DBNDD2Q9BQY9348
ZNF560NALF2O75949323
ZNF560SCML4Q8N228318
ZNF560C19orf33Q9GZP8312
ZNF560KRTAP8-1Q8IUC2312
ZNF560NRIP2Q9BQI9310
ZNF560CSAG1Q6PB30305
ZNF560CCNQQ8N1B3305
ZNF560TMEM130Q8N3G9300
ZNF560CYYR1Q96J86297
ZNF560SPESP1Q6UW49296
ZNF560TLCD4Q96MV1293
ZNF560GAS2L1Q99501291

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0JPL0, A6NK53, E7ETH6, E9Q8G5, O14628, P21506, P51508, Q09FC8, Q13360, Q2M218, Q2M3X9, Q2VY69, Q3KQV3, Q3SY52, Q4R882, Q5HY98, Q5REN4, Q5RES8, Q68DI1, Q6NX49, Q6P280, Q6PG37, Q6V9R5, Q6ZMW2, Q7Z340, Q86XU0, Q8IYI8, Q8N587, Q8N720, Q8N859, Q8NB42, Q8NDW4, Q8NEK5, Q8WXB4, Q96MR9, Q96MU6, Q96NG8, Q96NJ3, Q96SR6, Q9BR84

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance118
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1597 predictions. Top by Δscore:

VariantEffectΔscore
19:9468333:GC:Gacceptor_gain1.0000
19:9468334:CC:Cacceptor_gain1.0000
19:9468335:C:CAacceptor_loss1.0000
19:9468335:C:CCacceptor_gain1.0000
19:9468336:T:Aacceptor_loss1.0000
19:9468342:C:CTacceptor_gain1.0000
19:9468344:C:CTacceptor_gain1.0000
19:9468345:A:Tacceptor_gain1.0000
19:9469104:CCAA:Cdonor_gain1.0000
19:9469142:T:Cdonor_gain1.0000
19:9469626:TCA:Tdonor_loss1.0000
19:9469627:CA:Cdonor_loss1.0000
19:9469628:A:ACdonor_gain1.0000
19:9469628:A:AGdonor_loss1.0000
19:9469629:C:CCdonor_gain1.0000
19:9469629:C:CTdonor_loss1.0000
19:9469707:TAAC:Tacceptor_gain1.0000
19:9469708:AAC:Aacceptor_gain1.0000
19:9469709:AC:Aacceptor_gain1.0000
19:9469710:CC:Cacceptor_gain1.0000
19:9469711:C:CCacceptor_gain1.0000
19:9469713:G:Cacceptor_gain1.0000
19:9469713:G:GCacceptor_gain1.0000
19:9470387:CTTA:Cdonor_loss1.0000
19:9470390:A:ACdonor_gain1.0000
19:9470390:A:Tdonor_loss1.0000
19:9470390:AC:Adonor_gain1.0000
19:9470391:C:CGdonor_gain1.0000
19:9470391:CC:Cdonor_gain1.0000
19:9470391:CCT:Cdonor_gain1.0000

AlphaMissense

5237 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:9467204:G:CF581L0.994
19:9467204:G:TF581L0.994
19:9467206:A:GF581L0.994
19:9467708:A:CF413L0.993
19:9467708:A:TF413L0.993
19:9467710:A:GF413L0.993
19:9467288:G:CF553L0.987
19:9467288:G:TF553L0.987
19:9467290:A:GF553L0.987
19:9467792:G:CF385L0.987
19:9467792:G:TF385L0.987
19:9467794:A:GF385L0.987
19:9467120:G:CF609L0.983
19:9467120:G:TF609L0.983
19:9467122:A:GF609L0.983
19:9466616:A:CF777L0.980
19:9466616:A:TF777L0.980
19:9466618:A:GF777L0.980
19:9467765:A:CH394Q0.979
19:9467765:A:TH394Q0.979
19:9467456:A:CF497L0.978
19:9467456:A:TF497L0.978
19:9467458:A:GF497L0.978
19:9467681:A:CH422Q0.978
19:9467681:A:TH422Q0.978
19:9470483:G:CF119L0.978
19:9470483:G:TF119L0.978
19:9470485:A:GF119L0.978
19:9467187:A:GL587P0.977
19:9467429:A:CH506Q0.977

dbSNP variants (sampled 300 via entrez): RS1000002683 (19:9469416 A>C), RS1000020831 (19:9456136 A>C), RS1000110503 (19:9475810 G>A), RS1000156887 (19:9497727 A>G), RS1000186586 (19:9496839 G>A), RS1000194164 (19:9457770 G>A,T), RS1000203338 (19:9463438 T>C,G), RS1000222117 (19:9479148 C>G,T), RS1000242385 (19:9490004 T>G), RS1000294627 (19:9490304 C>A), RS1000315752 (19:9459022 G>A), RS1000317637 (19:9463145 G>A), RS1000516620 (19:9480026 G>A), RS1000564375 (19:9459365 C>G), RS1000628734 (19:9491421 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): prostate cancer (MONDO:0008315)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

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.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
arsenitedecreases expression, increases methylation1
bisphenol Sdecreases methylation1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Aflatoxin B1increases methylation1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_XW64HEK293 eGFP-ZNF560Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.