ZNF569

Summary

ZNF569 (zinc finger protein 569, HGNC:24737) is a protein-coding gene on chromosome 19q13.12, encoding Zinc finger protein 569 (Q5MCW4). 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 148266 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_152484

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24737
Approved symbol	ZNF569
Name	zinc finger protein 569
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32053, ZAP1, Zfp74
Ensembl gene	ENSG00000196437
Ensembl biotype	protein_coding
OMIM	613904
Entrez	148266

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 18 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000316950, ENST00000392149, ENST00000392150, ENST00000448051, ENST00000589833, ENST00000591073, ENST00000591710, ENST00000592490, ENST00000882774, ENST00000882775, ENST00000882776, ENST00000882777, ENST00000882778, ENST00000882779, ENST00000940356, ENST00000940357, ENST00000943077, ENST00000943078, ENST00000943079

RefSeq mRNA: 2 — MANE Select: NM_152484 NM_001330482, NM_152484

CCDS: CCDS12503, CCDS82341

Canonical transcript exons

ENST00000316950 — 6 exons

Exon	Start	End
ENSE00001364575	37465313	37465473
ENSE00001373173	37467084	37467444
ENSE00002485117	37425868	37425963
ENSE00003485929	37444907	37444964
ENSE00003791035	37426252	37426378
ENSE00003890725	37411157	37414419

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 87.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2702 / max 84.4849, expressed in 1556 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180714	3.5825	1331
180716	2.2337	941
180715	2.1340	986
180713	0.1912	80
180712	0.1286	41

Top tissues by expression

238 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	87.83	gold quality
sperm	CL:0000019	86.08	gold quality
oocyte	CL:0000023	85.89	gold quality
cortical plate	UBERON:0005343	85.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.81	gold quality
ganglionic eminence	UBERON:0004023	83.68	gold quality
secondary oocyte	CL:0000655	81.69	gold quality
ventricular zone	UBERON:0003053	81.25	gold quality
calcaneal tendon	UBERON:0003701	80.08	gold quality
right testis	UBERON:0004534	79.43	gold quality
left testis	UBERON:0004533	79.33	gold quality
testis	UBERON:0000473	78.90	gold quality
sural nerve	UBERON:0015488	77.84	gold quality
islet of Langerhans	UBERON:0000006	77.13	gold quality
cerebellar cortex	UBERON:0002129	74.57	gold quality
cerebellar hemisphere	UBERON:0002245	74.45	gold quality
prefrontal cortex	UBERON:0000451	74.29	gold quality
adrenal tissue	UBERON:0018303	74.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.26	gold quality
smooth muscle tissue	UBERON:0001135	74.09	gold quality
cerebellum	UBERON:0002037	73.89	gold quality
stromal cell of endometrium	CL:0002255	73.57	gold quality
pigmented layer of retina	UBERON:0001782	73.29	gold quality
right hemisphere of cerebellum	UBERON:0014890	73.24	gold quality
hypothalamus	UBERON:0001898	72.81	gold quality
muscle of leg	UBERON:0001383	72.69	gold quality
Brodmann (1909) area 9	UBERON:0013540	72.66	gold quality
gastrocnemius	UBERON:0001388	72.54	gold quality
anterior cingulate cortex	UBERON:0009835	72.34	gold quality
mucosa of paranasal sinus	UBERON:0005030	72.31	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-10	no	181.60
E-ANND-3	no	3.56

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
ETNK1
SLU7

miRNA regulators (miRDB)

86 targeting ZNF569, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-548A-3P	99.76	70.58	3524

Literature-anchored findings (GeneRIF, showing 1)

• ZNF569 protein may act as a transcriptional repressor that suppresses MAPK signaling pathway to mediate cellular functions (PMID:16793018)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:66472	ENSDARG00000075916
danio_rerio	si:ch211-148l7.4	ENSDARG00000094469
mus_musculus	Zfp74	ENSMUSG00000059975
rattus_norvegicus	Zfp74	ENSRNOG00000069539
drosophila_melanogaster	mld	FBGN0263490

Paralogs (36): ZNF302 (ENSG00000089335), ZNF184 (ENSG00000096654), CTCF (ENSG00000102974), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZNF497 (ENSG00000174586), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Zinc finger protein 569 — Q5MCW4 (reviewed: Q5MCW4)

All UniProt accessions (5): Q5MCW4, K7EJ12, K7EKE0, K7ELU1, K7ENQ2

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?
Q5MCW4-1	1	yes
Q5MCW4-2	2

RefSeq proteins (2): NP_001317411, NP_689697* (*=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

UniProt features (24 total): zinc finger region 18, sequence variant 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5MCW4-F1	75.49	0.21

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 112 (showing top): AGCTCCT_MIR28, STAT1_02, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER, YKACATTT_UNKNOWN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, STAT1_03, SNACANNNYSYAGA_UNKNOWN, ALX4_01, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, ARID5B_TARGET_GENES, CBX5_TARGET_GENES, CBX7_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, 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
RNA Polymerase II Transcription	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

2048 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF569	TRIM28	Q13263	981
ZNF569	ZUP1	Q96AP4	855
ZNF569	USP5	P45974	818
ZNF569	UBB	P02248	810
ZNF569	YOD1	Q5VVQ6	786
ZNF569	USP44	Q9H0E7	772
ZNF569	OTUD7A	Q8TE49	739
ZNF569	SETDB1	Q15047	673
ZNF569	ZPR1	O75312	670
ZNF569	CRBN	Q96SW2	659
ZNF569	HDAC6	Q9UBN7	653
ZNF569	UBA2	Q9UBT2	648
ZNF569	PHF20	Q9BVI0	638
ZNF569	NPLOC4	Q8TAT6	567
ZNF569	ZFAND5	O76080	552

IntAct

17 interactions, top by confidence:

A	B	Type	Score
ZNF569	KRT31	psi-mi:“MI:0915”(physical association)	0.720
KRT31	ZNF569	psi-mi:“MI:0915”(physical association)	0.720
KRT40	ZNF569	psi-mi:“MI:0915”(physical association)	0.560
ZNF569	KRT40	psi-mi:“MI:0915”(physical association)	0.560
TH	ZNF569	psi-mi:“MI:0915”(physical association)	0.560
ZNF569	CDC37	psi-mi:“MI:0915”(physical association)	0.400
CBX5	ZNF568	psi-mi:“MI:0914”(association)	0.350
STK24	PIK3C2A	psi-mi:“MI:0914”(association)	0.350
STK38L	SH3PXD2B	psi-mi:“MI:2364”(proximity)	0.270
ZNF569	KRT31	psi-mi:“MI:0915”(physical association)	0.000
TH	ZNF569	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): ZNF569 (Two-hybrid), ZNF569 (Two-hybrid), ZNF569 (Reconstituted Complex), ZNF569 (Two-hybrid), ZNF569 (Two-hybrid), ZNF569 (Two-hybrid), ZNF569 (Affinity Capture-RNA), ZNF569 (Affinity Capture-MS), ZNF569 (Affinity Capture-MS), ZNF569 (Affinity Capture-MS), ZNF569 (Affinity Capture-MS), ZNF569 (Affinity Capture-RNA), ZNF569 (Affinity Capture-MS)

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: 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1183 predictions. Top by Δscore:

Variant	Effect	Δscore
19:37425960:TAGC:T	acceptor_gain	1.0000
19:37425964:C:CC	acceptor_gain	1.0000
19:37426251:CCTA:C	donor_gain	1.0000
19:37426254:A:AC	donor_gain	1.0000
19:37426255:C:CC	donor_gain	1.0000
19:37469277:GAC:G	donor_gain	1.0000
19:37425863:CTAA:C	donor_loss	0.9900
19:37425865:AAC:A	donor_loss	0.9900
19:37425867:C:A	donor_loss	0.9900
19:37425891:T:TA	donor_gain	0.9900
19:37425894:T:TA	donor_gain	0.9900
19:37425960:TAGCC:T	acceptor_loss	0.9900
19:37425961:AGCC:A	acceptor_loss	0.9900
19:37425962:GC:G	acceptor_gain	0.9900
19:37425963:CC:C	acceptor_gain	0.9900
19:37425963:CCTG:C	acceptor_loss	0.9900
19:37425965:T:C	acceptor_loss	0.9900
19:37426246:TCTTA:T	donor_loss	0.9900
19:37426247:CTTA:C	donor_loss	0.9900
19:37426248:TTA:T	donor_loss	0.9900
19:37426249:TA:T	donor_loss	0.9900
19:37426250:A:C	donor_loss	0.9900
19:37426251:CCTAC:C	donor_loss	0.9900
19:37426377:CC:C	acceptor_gain	0.9900
19:37426378:CC:C	acceptor_gain	0.9900
19:37426379:C:CC	acceptor_gain	0.9900
19:37426427:T:TC	acceptor_gain	0.9900
19:37444902:TTTA:T	donor_loss	0.9900
19:37444903:TTA:T	donor_loss	0.9900
19:37444904:T:TG	donor_loss	0.9900

AlphaMissense

4645 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:37412729:G:C	F643L	0.998
19:37412729:G:T	F643L	0.998
19:37412731:A:G	F643L	0.998
19:37412897:G:C	F587L	0.998
19:37412897:G:T	F587L	0.998
19:37412899:A:G	F587L	0.998
19:37412981:G:C	F559L	0.998
19:37412981:G:T	F559L	0.998
19:37412983:A:G	F559L	0.998
19:37413233:A:C	F475L	0.998
19:37413233:A:T	F475L	0.998
19:37413235:A:G	F475L	0.998
19:37412645:G:C	F671L	0.997
19:37412645:G:T	F671L	0.997
19:37412647:A:G	F671L	0.997
19:37412813:G:C	F615L	0.997
19:37412813:G:T	F615L	0.997
19:37412815:A:G	F615L	0.997
19:37413065:G:C	F531L	0.997
19:37413065:G:T	F531L	0.997
19:37413067:A:G	F531L	0.997
19:37413216:A:G	L481P	0.997
19:37413401:G:C	F419L	0.997
19:37413401:G:T	F419L	0.997
19:37413403:A:G	F419L	0.997
19:37413569:G:C	F363L	0.997
19:37413569:G:T	F363L	0.997
19:37413571:A:G	F363L	0.997
19:37413737:G:C	F307L	0.997
19:37413737:G:T	F307L	0.997

dbSNP variants (sampled 300 via entrez): RS1000095520 (19:37463600 A>G), RS1000137171 (19:37456837 A>C,G), RS1000159930 (19:37417364 G>A,C,T), RS1000342424 (19:37437605 C>T), RS1000375132 (19:37437373 T>G), RS1000543001 (19:37430871 T>C), RS1000623143 (19:37444468 C>G), RS1000729222 (19:37410948 C>T), RS1000756132 (19:37418483 A>G), RS1000801628 (19:37465500 A>G), RS1000802066 (19:37445058 A>G), RS1000849434 (19:37418283 C>A,G,T), RS1000883589 (19:37430139 G>A), RS1000911410 (19:37451324 C>A,G,T), RS1000951963 (19:37457192 C>A)

Disease associations

OMIM: gene MIM:613904 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation	5
trichostatin A	affects cotreatment, decreases expression	2
sodium arsenite	decreases expression, increases expression	2
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	2
Acrolein	increases abundance, affects cotreatment, decreases expression	2
Ozone	increases abundance, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	affects cotreatment, increases methylation	1
avobenzone	increases 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	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, increases methylation	1
jinfukang	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Estradiol	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Permethrin	decreases expression	1
Volatile Organic Compounds	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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