ZNF587

Summary

ZNF587 (zinc finger protein 587, HGNC:30955) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 587 (Q96SQ5). 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 84914 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_032828

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30955
Approved symbol	ZNF587
Name	zinc finger protein 587
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZF6, FLJ14710, UBF-fl, FLJ20813
Ensembl gene	ENSG00000198466
Ensembl biotype	protein_coding
OMIM	621275
Entrez	84914

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000339656, ENST00000419854, ENST00000423137, ENST00000484707, ENST00000596433, ENST00000859086

RefSeq mRNA: 2 — MANE Select: NM_032828 NM_001204817, NM_032828

CCDS: CCDS12964, CCDS56110

Canonical transcript exons

ENST00000339656 — 3 exons

Exon	Start	End
ENSE00001409152	57858576	57865117
ENSE00003503170	57856104	57856233
ENSE00003652091	57849859	57850071

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 93.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7941 / max 139.8894, expressed in 1726 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177803	5.8776	1681
177805	1.9165	807

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pylorus	UBERON:0001166	93.60	gold quality
jejunal mucosa	UBERON:0000399	92.92	gold quality
cerebellar vermis	UBERON:0004720	92.76	gold quality
corpus epididymis	UBERON:0004359	92.38	gold quality
caput epididymis	UBERON:0004358	92.18	gold quality
cardia of stomach	UBERON:0001162	92.04	gold quality
cauda epididymis	UBERON:0004360	91.54	gold quality
superior surface of tongue	UBERON:0007371	91.37	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.94	gold quality
buccal mucosa cell	CL:0002336	90.75	gold quality
nipple	UBERON:0002030	90.08	gold quality
renal medulla	UBERON:0000362	89.62	gold quality
jejunum	UBERON:0002115	89.51	gold quality
trachea	UBERON:0003126	89.45	gold quality
oral cavity	UBERON:0000167	89.13	gold quality
colonic mucosa	UBERON:0000317	89.12	gold quality
superficial temporal artery	UBERON:0001614	88.73	gold quality
epithelium of nasopharynx	UBERON:0001951	88.23	gold quality
ventral tegmental area	UBERON:0002691	87.96	gold quality
pericardium	UBERON:0002407	87.82	gold quality
subthalamic nucleus	UBERON:0001906	87.79	gold quality
epithelium of mammary gland	UBERON:0003244	87.46	gold quality
mammary duct	UBERON:0001765	87.41	gold quality
pharyngeal mucosa	UBERON:0000355	87.35	gold quality
lower lobe of lung	UBERON:0008949	87.26	gold quality
inferior vagus X ganglion	UBERON:0005363	87.16	gold quality
superior vestibular nucleus	UBERON:0007227	87.08	gold quality
corpus callosum	UBERON:0002336	86.88	gold quality
lateral globus pallidus	UBERON:0002476	86.64	silver quality
upper leg skin	UBERON:0004262	86.58	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

194 targeting ZNF587, 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-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7F-5P	99.98	72.56	1784
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
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-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-4803	99.98	71.99	3117
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-4458	99.96	71.64	1650

Literature-anchored findings (GeneRIF, showing 2)

• MiRNA-4537 functions as a tumor suppressor in gastric cancer and increases the radiosensitivity of gastric cancer cells. (PMID:34670480)
• The long non-sacoding RNA TMEM147-AS1/miR-133b/ZNF587 axis regulates the Warburg effect and promotes prostatic carcinoma invasion and proliferation. (PMID:36181243)

Cross-species orthologs

0 orthologs

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391)

Protein

Protein identifiers

Zinc finger protein 587 — Q96SQ5 (reviewed: Q96SQ5)

All UniProt accessions (1): Q96SQ5

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?
Q96SQ5-1	1	yes
Q96SQ5-2	2

RefSeq proteins (2): NP_001191746, NP_116217* (*=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 (18 total): zinc finger region 13, chain 1, domain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96SQ5-F1	66.82	0.27

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 86 (showing top): CAGCAGG_MIR370, FISCHER_G2_M_CELL_CYCLE, MODULE_480, MODULE_301, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, CHANDRAN_METASTASIS_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MODULE_427, NUYTTEN_EZH2_TARGETS_DN, MODULE_192, CHANDRAN_METASTASIS_TOP50_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP

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

612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF587	CYSRT1	A8MQ03	589
ZNF587	ZBTB14	O43829	589
ZNF587	IKZF3	Q9UKT9	558
ZNF587	TRAF1	Q13077	433
ZNF587	YIPF1	Q9Y548	415
ZNF587	IKZF2	Q9UKS7	397
ZNF587	ZFYVE21	Q9BQ24	349
ZNF587	G3V325	G3V325	305
ZNF587	LRRC66	Q68CR7	297
ZNF587	AADAT	Q8N5Z0	289
ZNF587	TLCD2	A6NGC4	287
ZNF587	CCDC125	Q86Z20	286
ZNF587	KIAA1328	Q86T90	277
ZNF587	TRIM28	Q13263	275
ZNF587	GATD1	Q8NB37	271

IntAct

470 interactions, top by confidence:

A	B	Type	Score
ZNF587	PRPF31	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-5	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
TNS2	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
FSD2	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
STX11	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRT40	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	CEP70	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	TRIM41	psi-mi:“MI:0915”(physical association)	0.720
ZBTB8A	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	MDFI	psi-mi:“MI:0915”(physical association)	0.720
TRIM54	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
CEP44	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
MID2	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
PNMA2	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
PRPF31	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	STX11	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-7	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-9	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	TRAF1	psi-mi:“MI:0915”(physical association)	0.720
KRT40	ZNF587	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (161): ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid), ZNF587 (Two-hybrid)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A3KN32, B2RUI1, O43296, O75123, P10072, P17020, P17097, P51814, P52736, P52740, Q07230, Q08ER8, Q13398, Q14590, Q32KN0, Q3KQV3, Q3MIS6, Q4V8A8, Q5CZA5, Q5RBQ3, Q5RBX0, Q5RCD9, Q5RCX4, Q6GQR8, Q6NX45, Q6P9A3, Q6PK81, Q7TSH9, Q7TSI0, Q7Z7L9, Q86UD4, Q8BFS8, Q8BLB0, Q8IVP9, Q8IZ26, Q8N9F8

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 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	13	19.1×	9e-12

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	6
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

873 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57850069:CAG:C	donor_loss	1.0000
19:57850072:GTA:G	donor_loss	1.0000
19:57850073:T:G	donor_loss	0.9900
19:57853852:TTC:T	donor_gain	0.9900
19:57858570:TTTCA:T	acceptor_loss	0.9900
19:57858571:TTCAG:T	acceptor_loss	0.9900
19:57858572:TCAGG:T	acceptor_loss	0.9900
19:57858573:CA:C	acceptor_loss	0.9900
19:57858574:A:AG	acceptor_gain	0.9900
19:57858574:A:C	acceptor_loss	0.9900
19:57858575:G:GG	acceptor_gain	0.9900
19:57860196:A:T	donor_gain	0.9900
19:57858574:A:G	acceptor_loss	0.9800
19:57858575:G:GA	acceptor_loss	0.9800
19:57858575:GGTT:G	acceptor_gain	0.9800
19:57850072:G:GG	donor_gain	0.9700
19:57853885:AGCT:A	donor_gain	0.9700
19:57856229:GCTGG:G	donor_gain	0.9700
19:57860267:GTCT:G	donor_gain	0.9700
19:57860268:TCTT:T	donor_gain	0.9700
19:57850032:T:TA	donor_gain	0.9600
19:57850033:A:AA	donor_gain	0.9600
19:57856230:CTGGG:C	donor_loss	0.9600
19:57856231:TGGGT:T	donor_loss	0.9600
19:57856232:GG:G	donor_gain	0.9600
19:57856232:GGGT:G	donor_loss	0.9600
19:57856232:GGGTA:G	donor_loss	0.9600
19:57856233:GG:G	donor_gain	0.9600
19:57856233:GGT:G	donor_loss	0.9600
19:57856234:G:GA	donor_loss	0.9600

AlphaMissense

3829 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57859577:T:C	F389L	0.998
19:57859579:T:A	F389L	0.998
19:57859579:T:G	F389L	0.998
19:57859409:T:C	F333L	0.996
19:57859411:T:A	F333L	0.996
19:57859411:T:G	F333L	0.996
19:57859661:T:C	F417L	0.996
19:57859663:T:A	F417L	0.996
19:57859663:T:G	F417L	0.996
19:57859997:T:C	F529L	0.996
19:57859999:T:A	F529L	0.996
19:57859999:T:G	F529L	0.996
19:57859325:T:C	F305L	0.995
19:57859327:T:A	F305L	0.995
19:57859327:T:G	F305L	0.995
19:57859913:T:C	F501L	0.995
19:57859915:T:A	F501L	0.995
19:57859915:T:G	F501L	0.995
19:57859745:T:C	F445L	0.994
19:57859747:T:A	F445L	0.994
19:57859747:T:G	F445L	0.994
19:57860081:T:C	F557L	0.993
19:57860083:T:A	F557L	0.993
19:57860083:T:G	F557L	0.993
19:57859604:C:G	H398D	0.992
19:57859606:T:A	H398Q	0.992
19:57859606:T:G	H398Q	0.992
19:57859493:T:C	F361L	0.991
19:57859495:T:A	F361L	0.991
19:57859495:T:G	F361L	0.991

dbSNP variants (sampled 300 via entrez): RS1000050071 (19:57851076 G>A), RS1000292244 (19:57862517 G>A,T), RS1000663840 (19:57862703 A>G), RS1000994534 (19:57855146 T>C), RS1001038005 (19:57863351 C>CAG), RS1001049035 (19:57859578 T>C), RS1001078746 (19:57859316 G>A), RS1001383976 (19:57854787 T>A), RS1002000978 (19:57847927 C>T), RS1002992217 (19:57856899 G>A,T), RS1003080602 (19:57861302 T>C), RS1003424715 (19:57862289 T>C), RS1003653377 (19:57849549 G>A), RS1003723786 (19:57853819 C>T), RS1003737907 (19:57857694 G>A)

Disease associations

OMIM: gene MIM:621275 | 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
GCST005173_2	Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes	4.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Cadmium Chloride	increases abundance, increases expression	2
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
pyrimidifen	decreases expression	1
torcetrapib	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
picoxystrobin	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	affects methylation	1
Cadmium	increases abundance, increases expression	1
Coumestrol	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Plant Extracts	affects cotreatment, increases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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