ZNF561

Summary

ZNF561 (zinc finger protein 561, HGNC:28684) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 561 (Q8N587). 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 93134 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 98 total
• MANE Select transcript: NM_152289

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28684
Approved symbol	ZNF561
Name	zinc finger protein 561
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC45408
Ensembl gene	ENSG00000171469
Ensembl biotype	protein_coding
Entrez	93134

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 12 protein_coding, 6 retained_intron, 5 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000302851, ENST00000326044, ENST00000421525, ENST00000424629, ENST00000435550, ENST00000443819, ENST00000444519, ENST00000444611, ENST00000444802, ENST00000457965, ENST00000465974, ENST00000470932, ENST00000471053, ENST00000479943, ENST00000480167, ENST00000483768, ENST00000485150, ENST00000490893, ENST00000494276, ENST00000495503, ENST00000497409, ENST00000897545, ENST00000897546, ENST00000897547, ENST00000912474, ENST00000912475, ENST00000941679

RefSeq mRNA: 2 — MANE Select: NM_152289 NM_001330365, NM_152289

CCDS: CCDS12216, CCDS82286

Canonical transcript exons

ENST00000302851 — 6 exons

Exon	Start	End
ENSE00001632414	9607329	9611336
ENSE00001799811	9621162	9621232
ENSE00003472951	9614021	9614103
ENSE00003502625	9619432	9619582
ENSE00003671858	9617045	9617171
ENSE00003685656	9618091	9618179

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 93.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.2607 / max 227.7270, expressed in 1765 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179016	12.2607	1765

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	93.53	gold quality
smooth muscle tissue	UBERON:0001135	93.12	gold quality
colonic epithelium	UBERON:0000397	92.04	gold quality
islet of Langerhans	UBERON:0000006	91.40	gold quality
stromal cell of endometrium	CL:0002255	89.89	gold quality
rectum	UBERON:0001052	89.44	gold quality
esophagus mucosa	UBERON:0002469	89.39	gold quality
bone marrow cell	CL:0002092	89.29	gold quality
gall bladder	UBERON:0002110	89.19	gold quality
lower esophagus mucosa	UBERON:0035834	89.08	gold quality
pancreas	UBERON:0001264	88.61	gold quality
ganglionic eminence	UBERON:0004023	88.55	gold quality
cortical plate	UBERON:0005343	87.89	gold quality
body of pancreas	UBERON:0001150	87.65	gold quality
esophagus	UBERON:0001043	87.50	gold quality
right uterine tube	UBERON:0001302	87.08	gold quality
amniotic fluid	UBERON:0000173	87.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.05	gold quality
urinary bladder	UBERON:0001255	86.96	gold quality
adrenal tissue	UBERON:0018303	86.91	gold quality
right adrenal gland	UBERON:0001233	86.72	gold quality
calcaneal tendon	UBERON:0003701	86.55	gold quality
vagina	UBERON:0000996	86.51	gold quality
monocyte	CL:0000576	86.48	gold quality
body of uterus	UBERON:0009853	86.48	gold quality
descending thoracic aorta	UBERON:0002345	86.42	gold quality
leukocyte	CL:0000738	86.32	gold quality
endometrium	UBERON:0001295	86.13	gold quality
epithelial cell of pancreas	CL:0000083	86.12	gold quality
right adrenal gland cortex	UBERON:0035827	86.06	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-ENAD-21	yes	1383.89
E-CURD-7	yes	1377.76
E-ANND-3	yes	5.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

142 targeting ZNF561, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-17-5P	99.89	73.83	2665

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfx	ENSDARG00000074453
danio_rerio		ENSDARG00000098424
mus_musculus	Zfy2	ENSMUSG00000000103
mus_musculus	Zfy1	ENSMUSG00000053211
rattus_norvegicus	Zfy1	ENSRNOG00000053042

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 561 — Q8N587 (reviewed: Q8N587)

All UniProt accessions (9): A8KAD9, C9IZJ4, C9J7U2, C9JQP3, Q8N587, F2Z3H5, F8W7U5, F8WAU2, F8WBU1

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?
Q8N587-1	1	yes
Q8N587-2	2

RefSeq proteins (2): NP_001317294, NP_689502* (*=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 (17 total): zinc finger region 12, 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-Q8N587-F1	60.21	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): 273, 424

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 69 (showing top): HEIDENBLAD_AMPLICON_12P11_12_DN, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, CBX5_TARGET_GENES, DIDO1_TARGET_GENES, HMGA1_TARGET_GENES, HOXB4_TARGET_GENES, KLF7_TARGET_GENES, RFX7_TARGET_GENES, RLF_TARGET_GENES, RORA_TARGET_GENES, RYBP_TARGET_GENES

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), regulation of macromolecule metabolic process (GO:0060255), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (5): 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), 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 metabolic process	2
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
macromolecule metabolic process	1
primary metabolic 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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

578 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF561	MTHFSD	Q2M296	380
ZNF561	SP140L	Q9H930	369
ZNF561	ZFYVE28	Q9HCC9	368
ZNF561	INO80E	Q8NBZ0	323
ZNF561	ZFHX2	Q9C0A1	315
ZNF561	EXD3	Q8N9H8	308
ZNF561	NACC2	Q96BF6	304
ZNF561	BOLA3	Q53S33	298
ZNF561	PTGR1	Q14914	243
ZNF561	DPF2	Q92785	233
ZNF561	SLITRK1	Q96PX8	231
ZNF561	MELTF	P08582	228
ZNF561	ZBTB10	Q96DT7	220
ZNF561	ITPKB	P27987	208
ZNF561	ZBTB8A	Q96BR9	205

IntAct

9 interactions, top by confidence:

A	B	Type	Score
ZNF562	ISLR	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
STYK1	MYO1C	psi-mi:“MI:0914”(association)	0.350
ZNF561	PPM1G	psi-mi:“MI:0914”(association)	0.350
TEX19	ZNF316	psi-mi:“MI:0914”(association)	0.350
ZNF562	MDM2	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): ZNF561 (Affinity Capture-RNA), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-MS), ZNF561 (Affinity Capture-RNA)

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: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

940 predictions. Top by Δscore:

Variant	Effect	Δscore
19:9614104:C:CC	acceptor_gain	1.0000
19:9614116:A:T	acceptor_gain	1.0000
19:9618085:GCTTA:G	donor_loss	1.0000
19:9618086:CTTAC:C	donor_loss	1.0000
19:9618087:TTA:T	donor_loss	1.0000
19:9618088:TA:T	donor_loss	1.0000
19:9618089:A:T	donor_loss	1.0000
19:9618176:AACC:A	acceptor_gain	1.0000
19:9618177:ACC:A	acceptor_gain	1.0000
19:9618178:CC:C	acceptor_gain	1.0000
19:9618178:CCC:C	acceptor_gain	1.0000
19:9618179:CC:C	acceptor_gain	1.0000
19:9614014:ATCTT:A	donor_loss	0.9900
19:9614015:TCTTA:T	donor_loss	0.9900
19:9614016:CTTA:C	donor_loss	0.9900
19:9614017:TTA:T	donor_loss	0.9900
19:9614018:T:G	donor_loss	0.9900
19:9614019:A:T	donor_loss	0.9900
19:9614020:C:CG	donor_loss	0.9900
19:9614100:CATT:C	acceptor_gain	0.9900
19:9614110:T:C	acceptor_gain	0.9900
19:9614110:T:TC	acceptor_gain	0.9900
19:9614115:C:CT	acceptor_gain	0.9900
19:9617038:CTCTT:C	donor_loss	0.9900
19:9617039:TCTTA:T	donor_loss	0.9900
19:9617040:CTTA:C	donor_loss	0.9900
19:9617041:TTACC:T	donor_loss	0.9900
19:9617042:TA:T	donor_loss	0.9900
19:9617043:AC:A	donor_gain	0.9900
19:9617044:C:CG	donor_loss	0.9900

AlphaMissense

3216 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:9610287:A:C	F458L	0.997
19:9610287:A:T	F458L	0.997
19:9610289:A:G	F458L	0.997
19:9610371:A:C	F430L	0.997
19:9610371:A:T	F430L	0.997
19:9610373:A:G	F430L	0.997
19:9610623:A:C	F346L	0.996
19:9610623:A:T	F346L	0.996
19:9610625:A:G	F346L	0.996
19:9610332:A:C	H443Q	0.995
19:9610332:A:T	H443Q	0.995
19:9610339:C:G	R441P	0.995
19:9610342:A:G	L440P	0.993
19:9610344:G:C	H439Q	0.993
19:9610344:G:T	H439Q	0.993
19:9610539:G:C	F374L	0.993
19:9610539:G:T	F374L	0.993
19:9610541:A:G	F374L	0.993
19:9610707:G:C	F318L	0.993
19:9610707:G:T	F318L	0.993
19:9610709:A:G	F318L	0.993
19:9610288:A:G	F458S	0.992
19:9610314:G:C	F449L	0.992
19:9610314:G:T	F449L	0.992
19:9610316:A:G	F449L	0.992
19:9610354:A:G	L436P	0.992
19:9610455:G:C	F402L	0.992
19:9610455:G:T	F402L	0.992
19:9610457:A:G	F402L	0.992
19:9610428:A:C	H411Q	0.991

dbSNP variants (sampled 300 via entrez): RS1000193576 (19:9613596 G>A), RS1000215047 (19:9614225 G>A), RS1000380547 (19:9616737 A>C), RS1000403905 (19:9617458 A>C), RS1000463808 (19:9607328 A>G), RS1000467740 (19:9615225 T>C), RS1000527884 (19:9614967 T>C), RS1000867399 (19:9619358 G>C), RS1000894040 (19:9622535 G>A,T), RS1001158527 (19:9620750 T>G), RS1001224941 (19:9616732 C>G), RS1001390051 (19:9621599 G>A,C), RS1001734627 (19:9621842 G>C), RS1001775605 (19:9607139 A>T), RS1002141730 (19:9616570 C>A,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

1 associations (top):

Study	Trait	p-value
GCST008551_6	Simvastatin-induced myopathy	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression	5
sodium arsenite	decreases expression, increases abundance, increases expression	3
Formaldehyde	decreases expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Aflatoxin B1	increases expression	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
chloroacetaldehyde	affects expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Cidofovir	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Cisplatin	decreases expression	1
Coumestrol	decreases expression	1
Clodronic Acid	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Ifosfamide	decreases expression	1
Methyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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