ZNF586

Summary

ZNF586 (zinc finger protein 586, HGNC:25949) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 586 (Q9NXT0). 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 54807 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_017652

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25949
Approved symbol	ZNF586
Name	zinc finger protein 586
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20070
Ensembl gene	ENSG00000083828
Ensembl biotype	protein_coding
Entrez	54807

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000391702, ENST00000396150, ENST00000396154, ENST00000598183, ENST00000598885, ENST00000599802, ENST00000651718

RefSeq mRNA: 3 — MANE Select: NM_017652 NM_001077426, NM_001204814, NM_017652

CCDS: CCDS42640, CCDS56107, CCDS56108

Canonical transcript exons

ENST00000396154 — 3 exons

Exon	Start	End
ENSE00001658745	57778751	57780616
ENSE00003691136	57776543	57776669
ENSE00003843364	57769676	57769878

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 89.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2419 / max 110.0044, expressed in 1769 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177796	9.8063	1763
177795	0.4355	219

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	89.08	gold quality
monocyte	CL:0000576	86.25	gold quality
blood	UBERON:0000178	86.21	gold quality
mononuclear cell	CL:0000842	86.06	gold quality
leukocyte	CL:0000738	86.04	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.31	gold quality
granulocyte	CL:0000094	84.95	gold quality
ganglionic eminence	UBERON:0004023	84.39	gold quality
minor salivary gland	UBERON:0001830	84.37	gold quality
cortical plate	UBERON:0005343	84.12	gold quality
adrenal tissue	UBERON:0018303	84.07	gold quality
ventricular zone	UBERON:0003053	83.20	gold quality
bone marrow	UBERON:0002371	83.13	gold quality
bone marrow cell	CL:0002092	83.06	gold quality
colonic epithelium	UBERON:0000397	82.94	gold quality
gastrocnemius	UBERON:0001388	82.72	gold quality
muscle of leg	UBERON:0001383	82.34	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.11	gold quality
spleen	UBERON:0002106	81.94	gold quality
lower esophagus mucosa	UBERON:0035834	81.94	gold quality
right uterine tube	UBERON:0001302	81.92	gold quality
mouth mucosa	UBERON:0003729	81.89	gold quality
left ovary	UBERON:0002119	81.62	gold quality
saliva-secreting gland	UBERON:0001044	81.45	gold quality
right lobe of thyroid gland	UBERON:0001119	81.37	gold quality
calcaneal tendon	UBERON:0003701	81.35	gold quality
body of stomach	UBERON:0001161	81.22	gold quality
right ovary	UBERON:0002118	81.16	gold quality
apex of heart	UBERON:0002098	81.13	gold quality
mucosa of transverse colon	UBERON:0004991	80.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting ZNF586, 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-4262	100.00	73.26	3931
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-3922-3P	99.25	64.96	1136

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), 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), ZNF561 (ENSG00000171469), 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 586 — Q9NXT0 (reviewed: Q9NXT0)

All UniProt accessions (5): Q9NXT0, A0A494BZW3, M0QZ99, M0R166, M0R336

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 (3)

UniProt ID	Names	Canonical?
Q9NXT0-1	1	yes
Q9NXT0-2	2
Q9NXT0-3	3

RefSeq proteins (3): NP_001070894, NP_001191743, NP_060122* (*=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
IPR050717	C2H2-ZF_Transcription_Reg	Family

Pfam: PF00096, PF01352

UniProt features (19 total): zinc finger region 11, splice variant 3, sequence conflict 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NXT0-F1	73.63	0.35

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 79 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LEE_DIFFERENTIATING_T_LYMPHOCYTE, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ARID5B_TARGET_GENES, CBX5_TARGET_GENES, TRIP13_TARGET_GENES, ZNF577_TARGET_GENES, ZNF766_TARGET_GENES, MIR4262, MIR181A_5P_MIR181B_5P, MIR181D_5P, MIR181C_5P, MIR4306, MIR3692_3P

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892), regulation of DNA-templated transcription (GO:0006355)

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 DNA-templated transcription	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of RNA biosynthetic process	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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF586	C6orf141	Q5SZD1	446
ZNF586	EFCAB7	A8K855	374
ZNF586	SLC37A3	Q8NCC5	367
ZNF586	FBXO28	Q9NVF7	349
ZNF586	ITLN2	Q8WWU7	348
ZNF586	FIBCD1	Q8N539	348
ZNF586	UBL3	O95164	305
ZNF586	HERC4	Q5GLZ8	305
ZNF586	C8orf88	P0DMB2	299
ZNF586	FILIP1L	Q4L180	290
ZNF586	CSAD	Q9Y600	272
ZNF586	OXSM	Q9NWU1	252
ZNF586	LPXN	O60711	248
ZNF586	GLRX3	O76003	234
ZNF586	CENPM	Q9NSP4	230

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ZNF586	IFNA13	psi-mi:“MI:0914”(association)	0.530
ZNF586	GTF2IRD1	psi-mi:“MI:0915”(physical association)	0.400
MYC		psi-mi:“MI:0914”(association)	0.350
purL	ZNF586	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): ZNF586 (Two-hybrid), IFNA17 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA17 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), GTF2IRD1 (Affinity Capture-MS), ZNF586 (Positive Genetic), ZNF586 (Affinity Capture-RNA)

ESM2 similar proteins: A6NDX5, A8MQ14, B7Z6K7, C9JN71, O43361, P0CJ79, P0DKX0, P17017, P17021, P17027, P17035, P17039, P51522, Q02386, Q13106, Q14585, Q3SYV7, Q3ZCX4, Q4R4C7, Q4V348, Q52M93, Q5R9F0, Q5RB30, Q5SXM1, Q6P3V2, Q6P5C7, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZN57, Q76KX8, Q7Z340, Q86V71, Q86XN6, Q8N4W9, Q8N7Q3, Q8N8Z8, Q8TC21, Q8TF45

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

902 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57813287:AACTT:A	donor_loss	1.0000
19:57813288:ACTTA:A	donor_loss	1.0000
19:57813289:CTTA:C	donor_loss	1.0000
19:57813290:TTAC:T	donor_loss	1.0000
19:57813291:T:TG	donor_loss	1.0000
19:57813293:C:T	donor_loss	1.0000
19:57769876:CAGG:C	donor_loss	0.9900
19:57769879:G:GC	donor_loss	0.9900
19:57769880:T:A	donor_loss	0.9900
19:57776542:GAGCA:G	acceptor_gain	0.9900
19:57813286:CAACT:C	donor_loss	0.9900
19:57813292:A:AC	donor_gain	0.9900
19:57813292:AC:A	donor_gain	0.9900
19:57813293:C:CC	donor_gain	0.9900
19:57813293:CC:C	donor_gain	0.9900
19:57814706:ATTAC:A	donor_loss	0.9900
19:57814709:ACCTG:A	donor_loss	0.9900
19:57814710:C:A	donor_loss	0.9900
19:57813429:A:AC	acceptor_gain	0.9800
19:57769879:G:GG	donor_gain	0.9700
19:57776809:GGT:G	donor_gain	0.9700
19:57776810:GTG:G	donor_gain	0.9700
19:57776811:TGT:T	donor_gain	0.9700
19:57813429:A:C	acceptor_gain	0.9700
19:57769804:G:GT	donor_gain	0.9600
19:57813293:CCCAG:C	donor_gain	0.9600
19:57813419:CC:C	acceptor_gain	0.9600
19:57813420:CCTGT:C	acceptor_gain	0.9600
19:57813439:A:C	acceptor_gain	0.9600
19:57814830:CTCG:C	donor_gain	0.9600

AlphaMissense

2670 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57779314:T:C	F243L	0.995
19:57779316:T:A	F243L	0.995
19:57779316:T:G	F243L	0.995
19:57779647:T:C	F354L	0.995
19:57779649:T:A	F354L	0.995
19:57779649:T:G	F354L	0.995
19:57779482:T:C	F299L	0.994
19:57779484:T:A	F299L	0.994
19:57779484:T:G	F299L	0.994
19:57779563:T:C	F326L	0.994
19:57779565:T:A	F326L	0.994
19:57779565:T:G	F326L	0.994
19:57779398:T:C	F271L	0.993
19:57779400:T:A	F271L	0.993
19:57779400:T:G	F271L	0.993
19:57779731:T:C	F382L	0.991
19:57779733:T:A	F382L	0.991
19:57779733:T:G	F382L	0.991
19:57779501:T:C	L305P	0.989
19:57779230:T:C	F215L	0.988
19:57779232:T:A	F215L	0.988
19:57779232:T:G	F215L	0.988
19:57779333:T:C	L249P	0.987
19:57779343:C:A	H252Q	0.985
19:57779343:C:G	H252Q	0.985
19:57779513:A:C	Q309P	0.985
19:57779676:C:A	H363Q	0.985
19:57779676:C:G	H363Q	0.985
19:57779666:T:C	L360P	0.984
19:57779146:T:C	F187L	0.983

dbSNP variants (sampled 300 via entrez): RS1000041046 (19:57771882 T>A,C), RS1000052760 (19:57778010 C>A,T), RS1000445531 (19:57768397 A>C), RS1000751240 (19:57768097 G>A,C), RS1000841670 (19:57771029 C>T), RS1000991062 (19:57777282 T>A,C), RS1001103113 (19:57771330 A>G), RS1001195669 (19:57771509 C>T), RS1001493977 (19:57768436 C>T), RS1001749727 (19:57771815 A>G,T), RS1001854698 (19:57780099 A>G,T), RS1002520327 (19:57777345 A>G), RS1002752731 (19:57770340 G>A,T), RS1002759262 (19:57777887 C>G,T), RS1002831768 (19:57777670 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	increases abundance, increases expression, decreases expression	2
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	affects expression	1
azoxystrobin	decreases expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, decreases expression	1
pyrachlostrobin	decreases expression	1
bisphenol S	decreases methylation	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Nickel	decreases expression	1
Rotenone	decreases expression	1
Selenium	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation, increases expression	1
Vitamin E	affects cotreatment, decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin M1	decreases expression	1
Asbestos, Crocidolite	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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