ZNF534

Summary

ZNF534 (zinc finger protein 534, HGNC:26337) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 534 (Q76KX8). 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 147658 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_001143938

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26337
Approved symbol	ZNF534
Name	zinc finger protein 534
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25344
Ensembl gene	ENSG00000198633
Ensembl biotype	protein_coding
Entrez	147658

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000301085, ENST00000332323, ENST00000432303, ENST00000433050, ENST00000617900, ENST00000919700

RefSeq mRNA: 5 — MANE Select: NM_001143938 NM_001143938, NM_001143939, NM_001291368, NM_001291369, NM_001351679

CCDS: CCDS46165, CCDS46166, CCDS77347, CCDS77348

Canonical transcript exons

ENST00000433050 — 5 exons

Exon	Start	End
ENSE00002523292	52435081	52435209
ENSE00002528330	52433955	52434081
ENSE00002529148	52431408	52431489
ENSE00003916570	52429148	52429244
ENSE00003916813	52437732	52442499

Expression profiles

Bgee: expression breadth ubiquitous, 106 present calls, max score 86.05.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0827 / max 27.5476, expressed in 29 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177306	0.0371	19
177304	0.0343	12
177305	0.0113	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.21	gold quality
cortical plate	UBERON:0005343	66.09	gold quality
nucleus accumbens	UBERON:0001882	64.45	gold quality
putamen	UBERON:0001874	64.38	gold quality
caudate nucleus	UBERON:0001873	64.09	gold quality
cerebellar cortex	UBERON:0002129	63.98	gold quality
cerebellum	UBERON:0002037	63.87	gold quality
cerebellar hemisphere	UBERON:0002245	63.87	gold quality
superior frontal gyrus	UBERON:0002661	63.49	gold quality
primary visual cortex	UBERON:0002436	63.08	gold quality
right hemisphere of cerebellum	UBERON:0014890	62.55	gold quality
right uterine tube	UBERON:0001302	61.55	gold quality
ganglionic eminence	UBERON:0004023	59.67	gold quality
Brodmann (1909) area 9	UBERON:0013540	59.36	gold quality
prefrontal cortex	UBERON:0000451	59.18	gold quality
frontal cortex	UBERON:0001870	59.16	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.05	gold quality
right frontal lobe	UBERON:0002810	58.79	gold quality
cerebral cortex	UBERON:0000956	58.65	gold quality
brain	UBERON:0000955	58.59	gold quality
calcaneal tendon	UBERON:0003701	58.20	gold quality
temporal lobe	UBERON:0001871	58.16	gold quality
amygdala	UBERON:0001876	58.06	gold quality
anterior cingulate cortex	UBERON:0009835	57.71	gold quality
apex of heart	UBERON:0002098	57.31	gold quality
Ammon’s horn	UBERON:0001954	56.91	gold quality
hypothalamus	UBERON:0001898	56.86	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	55.24	gold quality
ventricular zone	UBERON:0003053	55.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.08

Regulation

Is transcription factor: no

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 534 — Q76KX8 (reviewed: Q76KX8)

Alternative names: KRAB domain only protein 3

All UniProt accessions (3): Q76KX8, Q1T7F5, Q1T7F6

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?
Q76KX8-1	1	yes
Q76KX8-2	2

RefSeq proteins (5): NP_001137410, NP_001137411, NP_001278297, NP_001278298, NP_001338608 (=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
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096, PF01352

UniProt features (20 total): zinc finger region 17, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q76KX8-F1	67.63	0.14

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 18 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HATADA_METHYLATED_IN_LUNG_CANCER_UP, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR548AW, MIR3059_5P, MIR4782_5P, MIR5706, MIR6839_5P, MIR378J, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, REACTOME_REGULATION_OF_ENDOGENOUS_RETROELEMENTS, REACTOME_REGULATION_OF_ENDOGENOUS_RETROELEMENTS_BY_KRAB_ZFP_PROTEINS, PULVER_FOREY_CELLCYCLE_ENRICHED_TFS_S1

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 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 (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF534	ZNF202	O95125	611
ZNF534	ZNF282	Q9UDV7	433
ZNF534	NANOG	Q9H9S0	431
ZNF534	ZNF777	Q9ULD5	416
ZNF534	ZKSCAN2	Q63HK3	414
ZNF534	A0A3B3IT14	A0A3B3IT14	407
ZNF534	FOXP1	Q9H334	407
ZNF534	ZNF398	Q8TD17	402
ZNF534	MTNAP1	Q9BSJ5	399
ZNF534	TMEM185B	Q9H7F4	399
ZNF534	FOXA1	P55317	394
ZNF534	GRAMD2A	Q8IUY3	371
ZNF534	PRAMEF5	Q5TYX0	359
ZNF534	SOX2	P48431	354
ZNF534	KLF17	Q5JT82	350

IntAct

12 interactions, top by confidence:

A	B	Type	Score
ZNF534	WDR83OS	psi-mi:“MI:0915”(physical association)	0.560
ZNF534	AGAP1	psi-mi:“MI:0915”(physical association)	0.560
C1QC	ZNF534	psi-mi:“MI:0915”(physical association)	0.560
M		psi-mi:“MI:0914”(association)	0.350
ZNF534	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF534	WDR83OS	psi-mi:“MI:0915”(physical association)	0.000
ZNF534	AGAP1	psi-mi:“MI:0915”(physical association)	0.000
ZNF534	C1QC	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): ZNF534 (Two-hybrid), ZNF534 (Two-hybrid), ZNF534 (Two-hybrid)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	101
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

681 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52431465:G:GT	donor_gain	0.9900
19:52431487:CAG:C	donor_loss	0.9900
19:52431489:GGT:G	donor_loss	0.9900
19:52431490:GTAA:G	donor_loss	0.9900
19:52431491:T:G	donor_loss	0.9900
19:52434042:G:T	donor_gain	0.9900
19:52434080:AG:A	donor_loss	0.9900
19:52434081:GGTGA:G	donor_loss	0.9900
19:52434082:G:T	donor_loss	0.9900
19:52435076:A:G	acceptor_gain	0.9900
19:52435184:G:GT	donor_gain	0.9900
19:52437730:A:AG	acceptor_gain	0.9900
19:52437731:G:GG	acceptor_gain	0.9900
19:52437833:GCT:G	donor_gain	0.9900
19:52431490:GTAAG:G	donor_gain	0.9800
19:52433950:TTTAG:T	acceptor_loss	0.9800
19:52433953:AG:A	acceptor_gain	0.9800
19:52433953:AGG:A	acceptor_gain	0.9800
19:52433954:GG:G	acceptor_gain	0.9800
19:52433954:GGG:G	acceptor_gain	0.9800
19:52434084:G:GG	donor_loss	0.9800
19:52437731:GAGAA:G	acceptor_gain	0.9800
19:52437973:A:AG	acceptor_gain	0.9800
19:52433953:A:AG	acceptor_gain	0.9700
19:52433954:G:GG	acceptor_gain	0.9700
19:52433954:GGGGC:G	acceptor_gain	0.9700
19:52437726:TTCTA:T	acceptor_loss	0.9700
19:52437727:TCTA:T	acceptor_loss	0.9700
19:52437728:CTAGA:C	acceptor_loss	0.9700
19:52437729:TA:T	acceptor_loss	0.9700

AlphaMissense

4430 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:52439135:T:C	F572L	0.993
19:52439137:C:A	F572L	0.993
19:52439137:C:G	F572L	0.993
19:52439219:T:C	F600L	0.993
19:52439221:C:A	F600L	0.993
19:52439221:C:G	F600L	0.993
19:52433988:T:C	F17L	0.991
19:52433990:C:A	F17L	0.991
19:52433990:C:G	F17L	0.991
19:52438883:T:C	F488L	0.991
19:52438885:C:A	F488L	0.991
19:52438885:C:G	F488L	0.991
19:52438734:T:C	L438P	0.990
19:52438799:T:C	F460L	0.990
19:52438801:C:A	F460L	0.990
19:52438801:C:G	F460L	0.990
19:52439051:T:C	F544L	0.990
19:52439053:C:A	F544L	0.990
19:52439053:C:G	F544L	0.990
19:52438463:T:C	F348L	0.989
19:52438465:C:A	F348L	0.989
19:52438465:C:G	F348L	0.989
19:52433989:T:C	F17S	0.987
19:52438715:T:C	F432L	0.987
19:52438717:T:A	F432L	0.987
19:52438717:T:G	F432L	0.987
19:52439142:G:C	R574P	0.986
19:52439387:T:C	F656L	0.984
19:52439389:T:A	F656L	0.984
19:52439389:T:G	F656L	0.984

dbSNP variants (sampled 300 via entrez): RS1000097548 (19:52433419 T>C,G), RS1000167071 (19:52448476 A>G), RS1000344767 (19:52431828 A>G), RS1000501818 (19:52449936 C>T), RS1000552894 (19:52433498 C>G,T), RS1000590960 (19:52452139 A>G), RS1000594941 (19:52449584 A>G), RS1000785484 (19:52428118 C>G), RS1000880700 (19:52446722 G>A), RS1000947164 (19:52440913 TC>T,TCC), RS1001159154 (19:52443274 G>T), RS1001362656 (19:52429411 T>G), RS1001435715 (19:52447714 G>A), RS1001478252 (19:52429183 G>A,C), RS1001563561 (19:52442723 G>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)

Descriptor	Name	Tree numbers
D011471	Prostatic Neoplasms	C04.588.945.440.770; 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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Benzo(a)pyrene	increases methylation	1
Lipopolysaccharides	affects response to substance, increases expression	1
Rifampin	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00029224	PHASE4	COMPLETED	Treatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997	PHASE4	COMPLETED	Open-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609	PHASE4	COMPLETED	The Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623	PHASE4	SUSPENDED	The Plenaxis® Experience Study
NCT00106392	PHASE4	COMPLETED	A Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029	PHASE4	UNKNOWN	MR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485	PHASE4	COMPLETED	Angelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219	PHASE4	COMPLETED	Zoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271	PHASE4	COMPLETED	Effect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146	PHASE4	COMPLETED	Study 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
NCT00242554	PHASE4	COMPLETED	Open-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098	PHASE4	COMPLETED	Docetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696	PHASE4	COMPLETED	Casodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139	PHASE4	COMPLETED	Effect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765	PHASE4	COMPLETED	Effects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690	PHASE4	COMPLETED	Evaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708	PHASE4	COMPLETED	Local Anesthesia for Prostate Biopsy
NCT00526331	PHASE4	COMPLETED	Evaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213	PHASE4	COMPLETED	Compare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330	PHASE4	TERMINATED	Dissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966	PHASE4	COMPLETED	Radical Prostatectomy and Perioperative Fluid Therapy
NCT00805701	PHASE4	COMPLETED	Study Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027	PHASE4	COMPLETED	Effect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269	PHASE4	UNKNOWN	Can Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277	PHASE4	COMPLETED	Study of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800	PHASE4	COMPLETED	Does Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199	PHASE4	COMPLETED	Global Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226	PHASE4	COMPLETED	Evaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563	PHASE4	COMPLETED	Randomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905	PHASE4	COMPLETED	Study to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672	PHASE4	COMPLETED	3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143	PHASE4	TERMINATED	Prospective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742	PHASE4	UNKNOWN	Comparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563	PHASE4	COMPLETED	Hydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874	PHASE4	COMPLETED	Efficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472	PHASE4	TERMINATED	Firmagon (Degarelix) Intermittent Therapy
NCT01547416	PHASE4	COMPLETED	The Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544	PHASE4	COMPLETED	The Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749	PHASE4	UNKNOWN	Evaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635	PHASE4	COMPLETED	Study of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer