ZNF564

Summary

ZNF564 (zinc finger protein 564, HGNC:31106) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 564 (Q8TBZ8). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity 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 located in nucleus.

Source: NCBI Gene 163050 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_144976

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31106
Approved symbol	ZNF564
Name	zinc finger protein 564
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC26914
Ensembl gene	ENSG00000249709
Ensembl biotype	protein_coding
Entrez	163050

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000339282, ENST00000416136, ENST00000427105, ENST00000465410, ENST00000596193

RefSeq mRNA: 1 — MANE Select: NM_144976 NM_144976

CCDS: CCDS42505

Canonical transcript exons

ENST00000339282 — 4 exons

Exon	Start	End
ENSE00001429098	12525373	12527916
ENSE00001529909	12551330	12551482
ENSE00003634566	12528304	12528364
ENSE00003682173	12528570	12528696

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 89.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2985 / max 137.5056, expressed in 1748 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179314	8.5044	1733
179315	0.7940	505

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	89.90	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.30	gold quality
colonic epithelium	UBERON:0000397	85.87	gold quality
corpus callosum	UBERON:0002336	85.73	gold quality
sural nerve	UBERON:0015488	83.35	gold quality
endometrium	UBERON:0001295	82.06	gold quality
mucosa of transverse colon	UBERON:0004991	81.55	gold quality
tonsil	UBERON:0002372	81.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.23	gold quality
skeletal muscle tissue	UBERON:0001134	80.93	gold quality
urinary bladder	UBERON:0001255	80.23	gold quality
muscle tissue	UBERON:0002385	79.99	gold quality
ventricular zone	UBERON:0003053	79.98	gold quality
leukocyte	CL:0000738	79.20	gold quality
rectum	UBERON:0001052	79.13	gold quality
monocyte	CL:0000576	79.11	gold quality
adrenal tissue	UBERON:0018303	79.08	gold quality
bone marrow cell	CL:0002092	78.91	gold quality
adult mammalian kidney	UBERON:0000082	78.80	gold quality
kidney	UBERON:0002113	78.78	gold quality
blood	UBERON:0000178	78.48	gold quality
uterine cervix	UBERON:0000002	78.36	gold quality
ganglionic eminence	UBERON:0004023	78.31	gold quality
lymph node	UBERON:0000029	78.25	gold quality
spleen	UBERON:0002106	78.16	gold quality
myometrium	UBERON:0001296	78.02	gold quality
body of uterus	UBERON:0009853	77.93	gold quality
granulocyte	CL:0000094	77.85	gold quality
muscle of leg	UBERON:0001383	77.66	gold quality
right lobe of thyroid gland	UBERON:0001119	77.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting ZNF564, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-190A-5P	99.54	71.45	933
HSA-MIR-190B-5P	99.54	71.40	925
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-1912-3P	99.32	67.40	936
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-3940-5P	99.14	65.26	493

Literature-anchored findings (GeneRIF, showing 1)

• Long non-coding RNA ZFAS1 alleviates bupivacaine-induced neurotoxicity by regulating the miR-421/zinc finger protein564 (ZNF564) axis. (PMID:34414857)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG14442	FBGN0029893
drosophila_melanogaster	CG14440	FBGN0029894

Paralogs (11): IKZF2 (ENSG00000030419), ZNF821 (ENSG00000102984), ZNF639 (ENSG00000121864), IKZF4 (ENSG00000123411), ZNF382 (ENSG00000161298), IKZF3 (ENSG00000161405), ZNF613 (ENSG00000176024), IKZF1 (ENSG00000185811), ZNF567 (ENSG00000189042), ZNF649 (ENSG00000198093), ZNF350 (ENSG00000256683)

Protein

Protein identifiers

Zinc finger protein 564 — Q8TBZ8 (reviewed: Q8TBZ8)

All UniProt accessions (4): C9JLM4, Q8TBZ8, F8WD42, M0QZN8

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 (1): NP_659413* (*=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

Pfam: PF00096, PF01352, PF13465, PF13912

UniProt features (18 total): zinc finger region 15, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TBZ8-F1	77.89	0.41

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 438

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 44 (showing top): chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, ZWANG_DOWN_BY_2ND_EGF_PULSE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, CREB3L4_TARGET_GENES, E2F2_TARGET_GENES, FEV_TARGET_GENES, GREB1_TARGET_GENES, H1_6_TARGET_GENES, PRKDC_TARGET_GENES, SALL4_TARGET_GENES, SOX3_TARGET_GENES

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 (GO:0003700), 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	2
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	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

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF564	DCAF5	Q96JK2	444
ZNF564	TRAPPC6B	Q86SZ2	434
ZNF564	YPEL1	O60688	432
ZNF564	SLC2A4RG	Q9NR83	381
ZNF564	HELB	Q8NG08	367
ZNF564	FOXS1	O43638	360
ZNF564	FOXJ2	Q9P0K8	317
ZNF564	SOX14	O95416	307
ZNF564	HORMAD2	Q8N7B1	291
ZNF564	TUT1	Q9H6E5	282
ZNF564	GIGYF2	Q6Y7W6	271
ZNF564	FCGBP	Q9Y6R7	271
ZNF564	MEF2B	Q02080	256
ZNF564	CKAP5	Q14008	247
ZNF564	ELK3	P41970	246

IntAct

143 interactions, top by confidence:

A	B	Type	Score
ZNF564	PPP1R16B	psi-mi:“MI:0915”(physical association)	0.740
ZNF564	ALAS1	psi-mi:“MI:0915”(physical association)	0.720
TRIM23	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	MDFI	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	MID2	psi-mi:“MI:0915”(physical association)	0.720
ALAS1	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	TRIM23	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-7	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	TRAF1	psi-mi:“MI:0915”(physical association)	0.720
MDFI	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
MID2	ZNF564	psi-mi:“MI:0915”(physical association)	0.720
ZNF564	MAGEA1	psi-mi:“MI:0915”(physical association)	0.670
MAGEA1	ZNF564	psi-mi:“MI:0915”(physical association)	0.670
ZNF564	MTUS2	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (56): ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid), ZNF564 (Two-hybrid)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	5	12.1×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

853 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12527912:GATTT:G	acceptor_gain	1.0000
19:12527913:ATTT:A	acceptor_gain	1.0000
19:12527914:TTT:T	acceptor_gain	1.0000
19:12527915:TT:T	acceptor_gain	1.0000
19:12527915:TTC:T	acceptor_loss	1.0000
19:12527916:TCTG:T	acceptor_loss	1.0000
19:12527917:C:CA	acceptor_loss	1.0000
19:12527917:C:CC	acceptor_gain	1.0000
19:12527918:T:A	acceptor_loss	1.0000
19:12527918:T:C	acceptor_loss	1.0000
19:12528564:CCTTA:C	donor_loss	1.0000
19:12528565:CTTA:C	donor_loss	1.0000
19:12528566:TTA:T	donor_loss	1.0000
19:12528567:TA:T	donor_loss	1.0000
19:12528568:A:AC	donor_gain	1.0000
19:12528568:A:AT	donor_loss	1.0000
19:12528569:C:CC	donor_gain	1.0000
19:12528569:CCTA:C	donor_gain	1.0000
19:12528694:GTCC:G	acceptor_loss	1.0000
19:12528695:TCC:T	acceptor_loss	1.0000
19:12528697:CTA:C	acceptor_loss	1.0000
19:12528697:CTAA:C	acceptor_loss	1.0000
19:12528707:CCAAA:C	acceptor_gain	1.0000
19:12528708:C:T	acceptor_gain	1.0000
19:12528713:A:C	acceptor_gain	1.0000
19:12551334:T:TA	donor_gain	1.0000
19:12551342:T:TA	donor_gain	1.0000
19:12527926:A:AC	acceptor_gain	0.9900
19:12527926:A:C	acceptor_gain	0.9900
19:12528316:C:A	donor_gain	0.9900

AlphaMissense

3704 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12526650:G:C	F486L	0.995
19:12526650:G:T	F486L	0.995
19:12526652:A:G	F486L	0.995
19:12526734:A:C	F458L	0.994
19:12526734:A:T	F458L	0.994
19:12526736:A:G	F458L	0.994
19:12526902:A:C	F402L	0.994
19:12526902:A:T	F402L	0.994
19:12526904:A:G	F402L	0.994
19:12527490:A:C	F206L	0.994
19:12527490:A:T	F206L	0.994
19:12527492:A:G	F206L	0.994
19:12526818:G:C	F430L	0.993
19:12526818:G:T	F430L	0.993
19:12526820:A:G	F430L	0.993
19:12527070:G:C	F346L	0.993
19:12527070:G:T	F346L	0.993
19:12527072:A:G	F346L	0.993
19:12527322:A:C	F262L	0.993
19:12527322:A:T	F262L	0.993
19:12527324:A:G	F262L	0.993
19:12527234:A:G	S292P	0.992
19:12527238:G:C	F290L	0.992
19:12527238:G:T	F290L	0.992
19:12527240:A:G	F290L	0.992
19:12526611:A:C	H499Q	0.991
19:12526611:A:T	H499Q	0.991
19:12526695:A:C	H471Q	0.991
19:12526695:A:T	H471Q	0.991
19:12526863:G:C	H415Q	0.991

dbSNP variants (sampled 300 via entrez): RS1000004564 (19:12550386 T>C,G), RS1000118934 (19:12531291 C>A,T), RS1000161973 (19:12547113 A>G), RS1000407186 (19:12531557 G>A), RS1000621817 (19:12541408 G>A), RS1000678501 (19:12553355 C>A,G,T), RS1000708741 (19:12547397 T>C), RS1001031391 (19:12537548 G>T), RS1001066047 (19:12552179 G>A), RS1001099598 (19:12541451 G>T), RS1001106373 (19:12537332 TTTC>T), RS1001182375 (19:12538496 G>A,T), RS1001187605 (19:12537911 T>G), RS1001318463 (19:12538135 A>G), RS1001344824 (19:12547616 G>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
trichostatin A	affects cotreatment, decreases expression	2
Formaldehyde	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
benzo(e)pyrene	increases methylation	1
resorcinol	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1
S-Nitrosoglutathione	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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