ZNF543

Summary

ZNF543 (zinc finger protein 543, HGNC:25281) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 543 (Q08ER8). 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 125919 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 133 total
• MANE Select transcript: NM_213598

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25281
Approved symbol	ZNF543
Name	zinc finger protein 543
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434H055
Ensembl gene	ENSG00000178229
Ensembl biotype	protein_coding
OMIM	616847
Entrez	125919

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000321545, ENST00000869765

RefSeq mRNA: 1 — MANE Select: NM_213598 NM_213598

CCDS: CCDS33130

Canonical transcript exons

ENST00000321545 — 4 exons

Exon	Start	End
ENSE00001223282	57326633	57326728
ENSE00001317786	57327704	57330770
ENSE00001415530	57320472	57320871
ENSE00002437212	57323682	57323808

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 83.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.2629 / max 57.2208, expressed in 1707 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177766	6.1063	1705
177767	0.1566	72

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.20	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.75	gold quality
cortical plate	UBERON:0005343	76.08	gold quality
ventricular zone	UBERON:0003053	75.78	gold quality
adrenal tissue	UBERON:0018303	75.05	gold quality
ganglionic eminence	UBERON:0004023	74.70	gold quality
calcaneal tendon	UBERON:0003701	73.57	gold quality
skeletal muscle tissue	UBERON:0001134	73.22	gold quality
corpus callosum	UBERON:0002336	72.04	gold quality
stromal cell of endometrium	CL:0002255	71.80	gold quality
islet of Langerhans	UBERON:0000006	71.67	gold quality
muscle tissue	UBERON:0002385	71.23	gold quality
tonsil	UBERON:0002372	69.43	gold quality
placenta	UBERON:0001987	69.32	gold quality
smooth muscle tissue	UBERON:0001135	68.61	gold quality
muscle of leg	UBERON:0001383	68.50	gold quality
lymph node	UBERON:0000029	68.36	gold quality
gastrocnemius	UBERON:0001388	68.15	gold quality
endometrium	UBERON:0001295	68.07	gold quality
hindlimb stylopod muscle	UBERON:0004252	68.07	gold quality
bone marrow cell	CL:0002092	67.94	silver quality
urinary bladder	UBERON:0001255	67.69	gold quality
ovary	UBERON:0000992	67.21	gold quality
left ovary	UBERON:0002119	66.81	gold quality
adrenal gland	UBERON:0002369	66.41	gold quality
bone marrow	UBERON:0002371	66.35	gold quality
skin of leg	UBERON:0001511	66.23	gold quality
zone of skin	UBERON:0000014	66.03	gold quality
esophagus mucosa	UBERON:0002469	65.79	gold quality
right ovary	UBERON:0002118	65.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting ZNF543, 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-7110-3P	100.00	73.18	2486
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220

Literature-anchored findings (GeneRIF, showing 2)

• Data indicate 3 variants in 3 novel genes myc target 1 protein (MYCT1), caspase recruitment domain family member 8 (CARD8) and zinc finger protein 543 (ZNF543), associated with familial IgA nephropathy (IgAN). (PMID:26095808)
• CRISPR/Cas9-Mediated Disruption of ZNF543 Gene: An Approach Toward Discovering Its Relation to TRIM28 Gene in Parkinson’s Disease. (PMID:35467255)

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 543 — Q08ER8 (reviewed: Q08ER8)

All UniProt accessions (1): Q08ER8

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 (1): NP_998763* (*=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 13, sequence variant 6, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q08ER8-F1	69.72	0.18

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 41 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, ZNF10_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR340_5P, MIR6809_3P, MIR338_5P, MIR7110_3P, MIR494_3P, MIR4672, MIR4319, MIR5195_3P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): 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), sequence-specific double-stranded DNA binding (GO:1990837)

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
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF543	GPATCH2L	Q9NWQ4	505
ZNF543	ARMCX5	Q6P1M9	480
ZNF543	OR4K2	Q8NGD2	480
ZNF543	OR7G3	Q8NG95	416
ZNF543	SVOPL	Q8N434	399
ZNF543	A8MYK1	A8MYK1	375
ZNF543	MRPL23	Q16540	359
ZNF543	GPR174	Q9BXC1	325
ZNF543	MYCT1	Q8N699	311
ZNF543	HIF1AN	Q9NWT6	257
ZNF543	DEFA4	P12838	254
ZNF543	PTBP3	O95758	247
ZNF543	RPL23A	P29316	243
ZNF543	RAET1E	Q8TD07	241
ZNF543	SGPL1	O95470	231

IntAct

13 interactions, top by confidence:

A	B	Type	Score
KRTAP10-7	ZNF543	psi-mi:“MI:0915”(physical association)	0.560
MCC	ZNF543	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	ZNF543	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF543	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF543	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF543	MCC	psi-mi:“MI:0915”(physical association)	0.000
ZNF543	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): KRTAP10-7 (Two-hybrid), ZNF543 (Affinity Capture-RNA), ZNF543 (Two-hybrid), KRTAP10-6 (Two-hybrid), ZC3H18 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), NKTR (Affinity Capture-MS), ZNF445 (Affinity Capture-MS), CENPB (Affinity Capture-MS), UBTF (Affinity Capture-MS), JPH1 (Affinity Capture-MS), ZNF708 (Affinity Capture-MS), FRMD6 (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), ZNF324 (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: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	119
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

387 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57323672:A:AG	acceptor_gain	1.0000
19:57323673:A:G	acceptor_gain	1.0000
19:57323678:CCA:C	acceptor_loss	1.0000
19:57323679:CAGG:C	acceptor_loss	1.0000
19:57323680:A:AG	acceptor_gain	1.0000
19:57323680:AG:A	acceptor_gain	1.0000
19:57323680:AGGT:A	acceptor_gain	1.0000
19:57323681:G:A	acceptor_loss	1.0000
19:57323681:G:GA	acceptor_gain	1.0000
19:57323681:GG:G	acceptor_gain	1.0000
19:57323681:GGT:G	acceptor_gain	1.0000
19:57323681:GGTG:G	acceptor_gain	1.0000
19:57323681:GGTGT:G	acceptor_gain	1.0000
19:57323769:G:GT	donor_gain	1.0000
19:57323804:TCTGG:T	donor_gain	1.0000
19:57323805:CTGG:C	donor_gain	1.0000
19:57323806:TGG:T	donor_gain	1.0000
19:57323807:GG:G	donor_gain	1.0000
19:57323807:GGG:G	donor_gain	1.0000
19:57323808:GG:G	donor_gain	1.0000
19:57323809:G:GG	donor_gain	1.0000
19:57326617:T:TA	acceptor_gain	1.0000
19:57326625:A:AG	acceptor_gain	1.0000
19:57326625:AT:A	acceptor_gain	1.0000
19:57326626:T:G	acceptor_gain	1.0000
19:57326626:T:TA	acceptor_gain	1.0000
19:57326629:A:AG	acceptor_gain	1.0000
19:57326629:ACAG:A	acceptor_gain	1.0000
19:57326630:C:G	acceptor_gain	1.0000
19:57326631:A:AC	acceptor_loss	1.0000

AlphaMissense

3984 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57328840:T:C	F460L	0.997
19:57328842:T:A	F460L	0.997
19:57328842:T:G	F460L	0.997
19:57329008:T:C	F516L	0.997
19:57329010:T:A	F516L	0.997
19:57329010:T:G	F516L	0.997
19:57328336:T:C	F292L	0.996
19:57328338:C:A	F292L	0.996
19:57328338:C:G	F292L	0.996
19:57328420:T:C	F320L	0.996
19:57328422:T:A	F320L	0.996
19:57328422:T:G	F320L	0.996
19:57328924:T:C	F488L	0.996
19:57328926:C:A	F488L	0.996
19:57328926:C:G	F488L	0.996
19:57328504:T:C	F348L	0.995
19:57328506:C:A	F348L	0.995
19:57328506:C:G	F348L	0.995
19:57328672:T:C	F404L	0.995
19:57328674:C:A	F404L	0.995
19:57328674:C:G	F404L	0.995
19:57328756:T:C	F432L	0.995
19:57328758:C:A	F432L	0.995
19:57328758:C:G	F432L	0.995
19:57328859:T:C	L466P	0.995
19:57329092:T:C	F544L	0.995
19:57329094:T:A	F544L	0.995
19:57329094:T:G	F544L	0.995
19:57328252:T:C	F264L	0.994
19:57328254:T:A	F264L	0.994

dbSNP variants (sampled 300 via entrez): RS1000102991 (19:57323784 A>G), RS1000267660 (19:57327058 G>A), RS1000293496 (19:57321186 C>T), RS1000324093 (19:57321401 C>T), RS1000432277 (19:57321332 C>T), RS1000613469 (19:57326968 A>C), RS1001167072 (19:57329910 C>T), RS1001207294 (19:57321078 G>A), RS1001490355 (19:57331215 C>T), RS1001675182 (19:57326037 T>C), RS1001720153 (19:57323954 C>T), RS1002147009 (19:57326290 G>A,T), RS1002370782 (19:57331010 C>T), RS1002854714 (19:57320112 T>C), RS1002908478 (19:57320311 G>C,T)

Disease associations

OMIM: gene MIM:616847 | 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
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
arsenite	decreases reaction, affects binding	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Cisplatin	decreases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methotrexate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	increases expression, affects cotreatment	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Antirheumatic Agents	increases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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