ZNF583

Summary

ZNF583 (zinc finger protein 583, HGNC:26427) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 583 (Q96ND8). 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 147949 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_152478

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26427
Approved symbol	ZNF583
Name	zinc finger protein 583
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31030
Ensembl gene	ENSG00000198440
Ensembl biotype	protein_coding
Entrez	147949

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 12 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000291598, ENST00000333201, ENST00000391778, ENST00000436972, ENST00000537943, ENST00000539211, ENST00000585612, ENST00000588635, ENST00000890730, ENST00000890731, ENST00000890732, ENST00000890733, ENST00000923221, ENST00000923222, ENST00000969490, ENST00000969491

RefSeq mRNA: 3 — MANE Select: NM_152478 NM_001159860, NM_001159861, NM_152478

CCDS: CCDS12943

Canonical transcript exons

ENST00000333201 — 5 exons

Exon	Start	End
ENSE00002203011	56404332	56404452
ENSE00002321587	56422891	56427364
ENSE00002487592	56414345	56414440
ENSE00003499018	56413959	56414085
ENSE00003653089	56407026	56407123

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 86.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3606 / max 162.8225, expressed in 1309 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177718	3.3606	1309

Top tissues by expression

245 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	86.67	gold quality
cortical plate	UBERON:0005343	84.30	gold quality
calcaneal tendon	UBERON:0003701	82.81	gold quality
ganglionic eminence	UBERON:0004023	82.33	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.29	gold quality
colonic epithelium	UBERON:0000397	78.51	gold quality
islet of Langerhans	UBERON:0000006	77.12	gold quality
right testis	UBERON:0004534	74.85	gold quality
prefrontal cortex	UBERON:0000451	74.18	gold quality
adrenal tissue	UBERON:0018303	74.18	gold quality
stromal cell of endometrium	CL:0002255	74.01	gold quality
ventricular zone	UBERON:0003053	73.84	gold quality
left testis	UBERON:0004533	73.73	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.38	gold quality
granulocyte	CL:0000094	73.10	gold quality
testis	UBERON:0000473	73.04	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.47	gold quality
smooth muscle tissue	UBERON:0001135	72.43	gold quality
muscle of leg	UBERON:0001383	72.29	gold quality
gastrocnemius	UBERON:0001388	72.29	gold quality
cerebellar cortex	UBERON:0002129	72.06	gold quality
popliteal artery	UBERON:0002250	71.95	gold quality
tibial artery	UBERON:0007610	71.95	gold quality
cerebellar hemisphere	UBERON:0002245	71.87	gold quality
anterior cingulate cortex	UBERON:0009835	71.80	gold quality
right coronary artery	UBERON:0001625	71.56	gold quality
artery	UBERON:0001637	71.37	gold quality
cerebellum	UBERON:0002037	71.34	gold quality
left ovary	UBERON:0002119	71.29	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting ZNF583, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4500	99.99	72.72	2367
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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp583	ENSMUSG00000030443
rattus_norvegicus	Zfp583	ENSRNOG00000034184

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), 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), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 583 — Q96ND8 (reviewed: Q96ND8)

Alternative names: Zinc finger protein L3-5

All UniProt accessions (3): Q96ND8, F5GZQ5, I3L0C4

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.

RefSeq proteins (3): NP_001153332, NP_001153333, NP_689691* (*=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 (19 total): zinc finger region 12, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96ND8-F1	71.72	0.45

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 62 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, TAATAAT_MIR126, GOZGIT_ESR1_TARGETS_DN, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, MIKKELSEN_MEF_LCP_WITH_H3K4ME3, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR520D_5P, MIR524_5P, MIR548D_3P, MIR548H_3P_MIR548Z, MIR548BB_3P, MIR548AC

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), 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
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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

284 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF583	TMEM247	A6NEH6	512
ZNF583	WDR17	Q8IZU2	507
ZNF583	BEND4	Q6ZU67	484
ZNF583	UQCC6	Q69YU5	478
ZNF583	CCDC81	Q6ZN84	464
ZNF583	ST6GALNAC3	Q8NDV1	420
ZNF583	BTG4	Q9NY30	407
ZNF583	ALX3	O95076	397
ZNF583	NWD2	Q9ULI1	387
ZNF583	WDR87	Q6ZQQ6	374
ZNF583	SMIM24	O75264	369
ZNF583	TRAPPC6B	Q86SZ2	369
ZNF583	ST6GALNAC5	Q9BVH7	368
ZNF583	NPTX1	Q15818	348
ZNF583	A0A2R8Y6X2	A0A2R8Y6X2	328

IntAct

5 interactions, top by confidence:

A	B	Type	Score
ZNF583		psi-mi:“MI:0915”(physical association)	0.490
APP	ZNF583	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): ZNF583 (Affinity Capture-MS), ZNF583 (Two-hybrid), ZNF583 (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, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

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	52
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1033 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56413955:TCAGG:T	acceptor_loss	1.0000
19:56413956:CAG:C	acceptor_loss	1.0000
19:56413957:AG:A	acceptor_gain	1.0000
19:56413957:AGG:A	acceptor_loss	1.0000
19:56413958:GG:G	acceptor_gain	1.0000
19:56414046:A:T	donor_gain	1.0000
19:56414083:TGGGT:T	donor_loss	1.0000
19:56414084:GG:G	donor_gain	1.0000
19:56414085:GG:G	donor_gain	1.0000
19:56414086:G:GG	donor_gain	1.0000
19:56414086:GT:G	donor_loss	1.0000
19:56421522:T:G	donor_gain	1.0000
19:56421522:T:TG	donor_gain	1.0000
19:56421526:G:GG	donor_gain	1.0000
19:56422889:A:AG	acceptor_gain	1.0000
19:56422890:G:GG	acceptor_gain	1.0000
19:56404427:G:GT	donor_gain	0.9900
19:56404521:GTGT:G	donor_gain	0.9900
19:56407024:A:AG	acceptor_gain	0.9900
19:56407025:G:GG	acceptor_gain	0.9900
19:56407025:GCTC:G	acceptor_gain	0.9900
19:56413957:A:AG	acceptor_gain	0.9900
19:56413958:G:GA	acceptor_gain	0.9900
19:56413958:GGAT:G	acceptor_gain	0.9900
19:56413958:GGATT:G	acceptor_gain	0.9900
19:56414069:GAGC:G	donor_gain	0.9900
19:56414072:C:G	donor_gain	0.9900
19:56414082:TTGG:T	donor_gain	0.9900
19:56422886:TTTAG:T	acceptor_loss	0.9900
19:56422887:TTA:T	acceptor_loss	0.9900

AlphaMissense

3807 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56423487:T:C	F277L	0.999
19:56423489:C:A	F277L	0.999
19:56423489:C:G	F277L	0.999
19:56423991:T:C	F445L	0.999
19:56423993:T:A	F445L	0.999
19:56423993:T:G	F445L	0.999
19:56424159:T:C	F501L	0.999
19:56424161:T:A	F501L	0.999
19:56424161:T:G	F501L	0.999
19:56423571:T:C	F305L	0.998
19:56423573:C:A	F305L	0.998
19:56423573:C:G	F305L	0.998
19:56423823:T:C	F389L	0.998
19:56423825:C:A	F389L	0.998
19:56423825:C:G	F389L	0.998
19:56423907:T:C	F417L	0.998
19:56423909:C:A	F417L	0.998
19:56423909:C:G	F417L	0.998
19:56424075:T:C	F473L	0.998
19:56424077:T:A	F473L	0.998
19:56424077:T:G	F473L	0.998
19:56423403:T:C	F249L	0.997
19:56423405:C:A	F249L	0.997
19:56423405:C:G	F249L	0.997
19:56423655:T:C	F333L	0.997
19:56423657:T:A	F333L	0.997
19:56423657:T:G	F333L	0.997
19:56423739:T:C	F361L	0.997
19:56423741:T:A	F361L	0.997
19:56423741:T:G	F361L	0.997

dbSNP variants (sampled 300 via entrez): RS1000269750 (19:56414551 CA>C), RS1000286757 (19:56421877 A>C), RS1000356289 (19:56402454 G>A), RS1000360040 (19:56422161 G>A), RS1000528512 (19:56403651 T>A,C), RS1000699172 (19:56408957 G>C), RS1000708727 (19:56408580 A>G), RS1000743015 (19:56406798 A>G), RS1000914086 (19:56416393 A>C), RS1000962978 (19:56403264 G>A), RS1001037726 (19:56424696 C>A,T), RS1001090248 (19:56424203 T>C), RS1001191892 (19:56421739 T>A), RS1001509660 (19:56422327 C>T), RS1001980143 (19:56422583 G>C)

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

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
terbufos	decreases methylation	1
arsenite	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Fonofos	decreases methylation	1
Parathion	decreases methylation	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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