ZNF566

Summary

ZNF566 (zinc finger protein 566, HGNC:25919) is a protein-coding gene on chromosome 19q13.12, encoding Zinc finger protein 566 (Q969W8). 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 located in membrane. Predicted to be active in nucleus.

Source: NCBI Gene 84924 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_001145344

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25919
Approved symbol	ZNF566
Name	zinc finger protein 566
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14779, MGC12515
Ensembl gene	ENSG00000186017
Ensembl biotype	protein_coding
Entrez	84924

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 12 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000392170, ENST00000424129, ENST00000427002, ENST00000434377, ENST00000452939, ENST00000460937, ENST00000472909, ENST00000480361, ENST00000493391, ENST00000494354, ENST00000587567, ENST00000915907, ENST00000915908, ENST00000915909, ENST00000915910, ENST00000968795

RefSeq mRNA: 5 — MANE Select: NM_001145344 NM_001145343, NM_001145344, NM_001145345, NM_001300970, NM_032838

CCDS: CCDS12494, CCDS46061, CCDS74346

Canonical transcript exons

ENST00000452939 — 5 exons

Exon	Start	End
ENSE00001115020	36472911	36473006
ENSE00001600800	36489486	36489561
ENSE00001796177	36445119	36450001
ENSE00002494351	36473332	36473458
ENSE00003668658	36476549	36476616

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 86.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0556 / max 66.4794, expressed in 1557 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180676	2.3734	1139
180677	1.3790	790
180679	0.9774	549
180678	0.3257	148

Top tissues by expression

234 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	86.76	gold quality
cortical plate	UBERON:0005343	84.12	gold quality
calcaneal tendon	UBERON:0003701	83.33	gold quality
ganglionic eminence	UBERON:0004023	83.19	gold quality
ventricular zone	UBERON:0003053	81.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.20	gold quality
adrenal tissue	UBERON:0018303	79.04	gold quality
colonic epithelium	UBERON:0000397	77.84	gold quality
islet of Langerhans	UBERON:0000006	77.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.72	gold quality
cerebellar hemisphere	UBERON:0002245	77.51	gold quality
cerebellar cortex	UBERON:0002129	77.37	gold quality
cerebellum	UBERON:0002037	76.19	gold quality
stromal cell of endometrium	CL:0002255	75.89	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.74	gold quality
muscle of leg	UBERON:0001383	75.44	gold quality
smooth muscle tissue	UBERON:0001135	75.35	gold quality
gastrocnemius	UBERON:0001388	75.10	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	75.04	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.62	gold quality
mucosa of stomach	UBERON:0001199	74.56	gold quality
left uterine tube	UBERON:0001303	74.34	gold quality
left adrenal gland	UBERON:0001234	74.11	gold quality
granulocyte	CL:0000094	73.99	gold quality
left adrenal gland cortex	UBERON:0035825	73.81	gold quality
anterior cingulate cortex	UBERON:0009835	73.61	gold quality
descending thoracic aorta	UBERON:0002345	73.57	gold quality
lower esophagus muscularis layer	UBERON:0035833	73.56	gold quality
lower esophagus	UBERON:0013473	73.55	gold quality
prefrontal cortex	UBERON:0000451	73.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	136.36
E-ANND-3	no	4.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

176 targeting ZNF566, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
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-340-5P	100.00	72.50	4437
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4775	99.98	75.00	6394
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-373-5P	99.98	75.36	4753

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp566	ENSMUSG00000078768
rattus_norvegicus	Zfp566	ENSRNOG00000048138
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), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 566 — Q969W8 (reviewed: Q969W8)

All UniProt accessions (5): Q969W8, B4DRR6, C9J2D3, C9J6X1, K7EQC1

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?
Q969W8-1	1	yes
Q969W8-2	2

RefSeq proteins (5): NP_001138815, NP_001138816, NP_001138817, NP_001287899, NP_116227 (=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352, PF13465

UniProt features (13 total): zinc finger region 8, cross-link 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969W8-F1	68.05	0.21

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 (2): 314, 328

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 115 (showing top): MODULE_255, GCM_ZNF198, MODULE_317, GCM_PPM1D, GCM_SUFU, WEBER_METHYLATED_IN_COLON_CANCER, MODULE_69, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_37, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BANP_TARGET_GENES, IRF5_TARGET_GENES, NFE2L1_TARGET_GENES, SUPT16H_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 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 (2): nucleus (GO:0005634), membrane (GO:0016020)

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
cellular anatomical structure	1

Protein interactions and networks

STRING

508 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF566	PDZK1IP1	Q13113	477
ZNF566	MBD3L3	A6NE82	431
ZNF566	ZNF608	Q9ULD9	375
ZNF566	C8orf89	P0DMQ9	375
ZNF566	ZFHX3	Q15911	370
ZNF566	SP140L	Q9H930	322
ZNF566	ZNF804A	Q7Z570	311
ZNF566	PITX2	Q99697	310
ZNF566	GMEB1	Q9Y692	305
ZNF566	ENTPD6	O75354	290
ZNF566	INO80E	Q8NBZ0	290
ZNF566	FAM133A	Q8N9E0	276
ZNF566	CMC2	Q9NRP2	266
ZNF566	ETV7	Q9Y603	256
ZNF566	SACK1B	Q5T0W9	248

IntAct

23 interactions, top by confidence:

A	B	Type	Score
EXOC8	ZNF566	psi-mi:“MI:0915”(physical association)	0.560
MAGOHB	ZNF566	psi-mi:“MI:0915”(physical association)	0.560
ZNF566	MAGOHB	psi-mi:“MI:0915”(physical association)	0.560
ZNF566	KIF9	psi-mi:“MI:0915”(physical association)	0.560
ZNF566	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
Trim28	FTH1	psi-mi:“MI:0915”(physical association)	0.400
ZNF566	KIF2C	psi-mi:“MI:0915”(physical association)	0.370
SPATA20	SCRN3	psi-mi:“MI:0914”(association)	0.350
CBX5	ZNF568	psi-mi:“MI:0914”(association)	0.350
ZNF566	IPO8	psi-mi:“MI:0914”(association)	0.350
SPATA20	HDAC4	psi-mi:“MI:0914”(association)	0.350
TRIM63	ZNF566	psi-mi:“MI:0915”(physical association)	0.000
TRIM55	ZNF566	psi-mi:“MI:0915”(physical association)	0.000
KIF9	ZNF566	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Synthetic Lethality), ZNF566 (Two-hybrid), ZNF566 (Two-hybrid), ZNF566 (Two-hybrid), ZNF566 (Two-hybrid), ZNF566 (Two-hybrid), ZNF566 (Proximity Label-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS), ZNF566 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1079 predictions. Top by Δscore:

Variant	Effect	Δscore
19:36450002:C:CC	acceptor_gain	1.0000
19:36473326:CCTTA:C	donor_loss	1.0000
19:36473327:CTT:C	donor_loss	1.0000
19:36473328:TTA:T	donor_loss	1.0000
19:36473329:TA:T	donor_loss	1.0000
19:36473330:A:AT	donor_loss	1.0000
19:36473330:AC:A	donor_gain	1.0000
19:36473331:CC:C	donor_gain	1.0000
19:36449997:CAGGA:C	acceptor_gain	0.9900
19:36449998:AGGA:A	acceptor_gain	0.9900
19:36449999:GGA:G	acceptor_gain	0.9900
19:36449999:GGAC:G	acceptor_loss	0.9900
19:36450000:GA:G	acceptor_gain	0.9900
19:36450000:GAC:G	acceptor_loss	0.9900
19:36450001:AC:A	acceptor_loss	0.9900
19:36473011:T:C	acceptor_gain	0.9900
19:36473330:A:AC	donor_gain	0.9900
19:36473331:C:CC	donor_gain	0.9900
19:36473456:CTC:C	acceptor_gain	0.9900
19:36473458:CCTGG:C	acceptor_loss	0.9900
19:36473460:T:C	acceptor_loss	0.9900
19:36476612:TAGAG:T	acceptor_gain	0.9900
19:36476617:C:CC	acceptor_gain	0.9900
19:36481737:A:T	acceptor_gain	0.9900
19:36450003:T:C	acceptor_loss	0.9800
19:36473011:T:TC	acceptor_gain	0.9800
19:36473459:C:CC	acceptor_gain	0.9800
19:36476542:ATCT:A	donor_loss	0.9800
19:36476543:TCTCA:T	donor_loss	0.9800
19:36476544:CTCAC:C	donor_loss	0.9800

AlphaMissense

1558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:36473377:A:C	Y31D	0.981
19:36473400:A:G	L23P	0.979
19:36473408:C:A	W20C	0.977
19:36473408:C:G	W20C	0.977
19:36449610:A:C	F208L	0.976
19:36449610:A:T	F208L	0.976
19:36449612:A:G	F208L	0.976
19:36473410:A:G	W20R	0.974
19:36473410:A:T	W20R	0.974
19:36473424:A:G	F15S	0.969
19:36473343:A:G	L42P	0.967
19:36449585:G:C	H217D	0.963
19:36449583:A:C	H217Q	0.955
19:36449583:A:T	H217Q	0.955
19:36473376:T:G	Y31S	0.952
19:36449553:A:C	F227L	0.949
19:36449553:A:T	F227L	0.949
19:36449555:A:G	F227L	0.949
19:36473423:G:C	F15L	0.947
19:36473423:G:T	F15L	0.947
19:36473425:A:G	F15L	0.947
19:36473409:C:G	W20S	0.943
19:36449581:T:G	Q218P	0.942
19:36473444:G:C	F8L	0.940
19:36473444:G:T	F8L	0.940
19:36473446:A:G	F8L	0.940
19:36449539:C:G	C232S	0.938
19:36449540:A:T	C232S	0.938
19:36473377:A:T	Y31N	0.938
19:36449538:A:C	C232W	0.937

dbSNP variants (sampled 300 via entrez): RS1000054786 (19:36469656 G>A), RS1000104729 (19:36459499 C>T), RS1000282859 (19:36453117 CA>C,CAA,CAAA), RS1000461785 (19:36449706 A>G), RS1000612846 (19:36477778 T>C), RS1000663525 (19:36482148 C>A), RS1000666625 (19:36477468 A>T), RS1000690060 (19:36465053 C>T), RS1000777970 (19:36482306 C>T), RS1000781060 (19:36478957 G>A), RS1000873400 (19:36483984 T>C,G), RS1000940792 (19:36467924 G>A), RS1001043749 (19:36446534 C>G), RS1001060139 (19:36468097 A>G), RS1001069610 (19:36489766 C>A,G,T)

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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
Vorinostat	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Nickel	decreases expression	1
Oxygen	decreases expression	1
Testosterone	increases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Tretinoin	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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