ZNF563

Summary

ZNF563 (zinc finger protein 563, HGNC:30498) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 563 (Q8TA94). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 147837 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 87 total
• MANE Select transcript: NM_145276

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30498
Approved symbol	ZNF563
Name	zinc finger protein 563
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34797
Ensembl gene	ENSG00000188868
Ensembl biotype	protein_coding
Entrez	147837

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000293725, ENST00000594577, ENST00000595977, ENST00000601858, ENST00000873252

RefSeq mRNA: 2 — MANE Select: NM_145276 NM_001363608, NM_145276

CCDS: CCDS12270, CCDS86706

Canonical transcript exons

ENST00000293725 — 4 exons

Exon	Start	End
ENSE00001185291	12317477	12319833
ENSE00001727359	12321272	12321332
ENSE00001831571	12333480	12333633
ENSE00003661839	12322585	12322711

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 85.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.2155 / max 133.7604, expressed in 1288 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179300	1.6820	644
179301	0.8778	446
179303	0.6848	426
179302	0.6219	366
179299	0.3098	149
179298	0.0392	11

Top tissues by expression

225 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	85.84	gold quality
left testis	UBERON:0004533	79.55	gold quality
calcaneal tendon	UBERON:0003701	78.67	gold quality
right testis	UBERON:0004534	78.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.97	gold quality
testis	UBERON:0000473	77.31	gold quality
right lobe of liver	UBERON:0001114	76.05	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.42	gold quality
right atrium auricular region	UBERON:0006631	73.06	gold quality
stromal cell of endometrium	CL:0002255	72.90	gold quality
cardiac atrium	UBERON:0002081	72.33	gold quality
apex of heart	UBERON:0002098	72.15	gold quality
descending thoracic aorta	UBERON:0002345	72.12	gold quality
left lobe of thyroid gland	UBERON:0001120	71.28	gold quality
islet of Langerhans	UBERON:0000006	71.14	gold quality
skin of leg	UBERON:0001511	71.05	gold quality
right adrenal gland cortex	UBERON:0035827	71.02	gold quality
right adrenal gland	UBERON:0001233	70.92	gold quality
left adrenal gland	UBERON:0001234	70.84	gold quality
thyroid gland	UBERON:0002046	70.48	gold quality
heart left ventricle	UBERON:0002084	70.34	gold quality
left adrenal gland cortex	UBERON:0035825	70.30	gold quality
thoracic aorta	UBERON:0001515	70.26	gold quality
ascending aorta	UBERON:0001496	70.21	gold quality
right lobe of thyroid gland	UBERON:0001119	70.15	gold quality
metanephros cortex	UBERON:0010533	70.15	gold quality
skin of abdomen	UBERON:0001416	70.10	gold quality
liver	UBERON:0002107	70.04	gold quality
ectocervix	UBERON:0012249	69.89	gold quality
aorta	UBERON:0000947	69.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting ZNF563, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6873-3P	100.00	71.42	2626
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-433-3P	99.98	69.37	1203
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6516-3P	99.65	68.57	1238
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp961	ENSMUSG00000052446
rattus_norvegicus	Zfp617	ENSRNOG00000049856

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 563 — Q8TA94 (reviewed: Q8TA94)

All UniProt accessions (4): A0A0C4DGQ9, Q8TA94, M0R1L6, M0R1Q6

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?
Q8TA94-1	1	yes
Q8TA94-2	2

RefSeq proteins (2): NP_001350537, NP_660319* (*=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
IPR050329	GLI_C2H2-zinc-finger	Family

Pfam: PF00096, PF01352

UniProt features (16 total): zinc finger region 12, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TA94-F1	70.27	0.13

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 63 (showing top): TGGAAA_NFAT_Q4_01, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ACACTGG_MIR199A_MIR199B, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, HEY2_TARGET_GENES, PRKDC_TARGET_GENES, SUPT16H_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF350_TARGET_GENES, MIR153_5P, MIR6867_5P, MIR4262

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), transcription cis-regulatory region binding (GO:0000976), 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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
positive regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
transition metal ion binding	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF563	DECR2	Q9NUI1	519
ZNF563	VPS33A	Q96AX1	507
ZNF563	FBF1	Q8TES7	507
ZNF563	SLC17A9	Q9BYT1	507
ZNF563	LRTM3	Q8NDH2	503
ZNF563	A0A2R8YFG2	A0A2R8YFG2	500
ZNF563	ITSN2	Q9NZM3	457
ZNF563	CLCN3	P51790	454
ZNF563	EXOSC10	Q01780	447
ZNF563	PTK6	Q13882	445
ZNF563	RUVBL2	Q9Y230	443
ZNF563	NALCN	Q8IZF0	394
ZNF563	CDH8	P55286	383
ZNF563	COL9A3	Q14050	383
ZNF563	A0A090J7P6	A0A090J7P6	374

IntAct

8 interactions, top by confidence:

A	B	Type	Score
KRTAP10-6	ZNF563	psi-mi:“MI:0915”(physical association)	0.560
ZNF563	LRP4	psi-mi:“MI:0914”(association)	0.530
SCRIB	ZNF563	psi-mi:“MI:0915”(physical association)	0.400
ECE1	ZNF563	psi-mi:“MI:0915”(physical association)	0.370
ZNF563	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): ZNF563 (Synthetic Lethality), SHCBP1 (Affinity Capture-MS), SORL1 (Affinity Capture-MS), LRP1B (Affinity Capture-MS), UBE2O (Affinity Capture-MS), LTBP4 (Affinity Capture-MS), ERBB2IP (Affinity Capture-MS), LRP4 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), ZNF563 (Two-hybrid), LTBP4 (Affinity Capture-MS), LRP4 (Affinity Capture-MS), SORL1 (Affinity Capture-MS), SHCBP1 (Affinity Capture-MS), UBE2O (Affinity Capture-MS)

ESM2 similar proteins: A6NP11, B4DXR9, O43361, O95780, P0CJ79, P0DKX0, P17021, P17024, P17035, P51508, P52740, P52741, P58317, Q02386, Q0VGE8, Q13106, Q13360, Q13398, Q5JVG2, Q5RBQ3, Q5RES8, Q5TYW1, Q68DI1, Q68EA5, Q6NX49, Q6P9A1, Q6P9A3, Q6PDB4, Q6ZN06, Q76KX8, Q7L945, Q7Z340, Q86T29, Q8BZW4, Q8IW36, Q8N823, Q8N8Z8, Q8NEP9, Q8TA94, Q8TC21

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	78
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

657 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12319312:C:CC	acceptor_gain	1.0000
19:12322578:T:TA	donor_gain	1.0000
19:12322583:A:AC	donor_gain	1.0000
19:12322584:C:CT	donor_gain	1.0000
19:12322588:T:C	donor_gain	1.0000
19:12322722:CCACA:C	acceptor_gain	1.0000
19:12322723:C:CT	acceptor_gain	1.0000
19:12322723:C:T	acceptor_gain	1.0000
19:12322725:C:CT	acceptor_gain	1.0000
19:12322726:A:C	acceptor_gain	1.0000
19:12322579:CCTTA:C	donor_loss	0.9900
19:12322580:CTTA:C	donor_loss	0.9900
19:12322581:TTA:T	donor_loss	0.9900
19:12322582:TA:T	donor_loss	0.9900
19:12322583:A:C	donor_loss	0.9900
19:12322585:TTA:T	donor_gain	0.9900
19:12322586:TAT:T	donor_gain	0.9900
19:12322587:A:AC	donor_gain	0.9900
19:12322587:ATA:A	donor_gain	0.9900
19:12322625:T:C	donor_gain	0.9900
19:12322718:C:CT	acceptor_gain	0.9900
19:12322730:A:C	acceptor_gain	0.9900
19:12333492:T:TA	donor_gain	0.9900
19:12333513:C:CA	donor_gain	0.9900
19:12322574:ATCAT:A	donor_gain	0.9800
19:12322584:CT:C	donor_gain	0.9800
19:12322584:CTTAT:C	donor_gain	0.9800
19:12322600:T:TA	donor_gain	0.9800
19:12322708:CGTC:C	acceptor_gain	0.9800
19:12322709:GTCCT:G	acceptor_gain	0.9800

AlphaMissense

3201 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12318987:A:C	F346L	0.993
19:12318987:A:T	F346L	0.993
19:12318989:A:G	F346L	0.993
19:12318819:A:C	F402L	0.991
19:12318819:A:T	F402L	0.991
19:12318821:A:G	F402L	0.991
19:12319155:G:C	F290L	0.991
19:12319155:G:T	F290L	0.991
19:12319157:A:G	F290L	0.991
19:12319071:A:C	F318L	0.990
19:12319071:A:T	F318L	0.990
19:12319073:A:G	F318L	0.990
19:12318955:C:G	R357P	0.988
19:12318876:G:C	H383Q	0.985
19:12318876:G:T	H383Q	0.985
19:12319323:A:C	F234L	0.985
19:12319323:A:T	F234L	0.985
19:12319325:A:G	F234L	0.985
19:12318888:G:C	S379R	0.983
19:12318888:G:T	S379R	0.983
19:12318890:T:G	S379R	0.983
19:12319044:G:C	H327Q	0.981
19:12319044:G:T	H327Q	0.981
19:12318780:G:C	H415Q	0.978
19:12318780:G:T	H415Q	0.978
19:12322677:A:G	F13S	0.977
19:12318948:G:C	H359Q	0.976
19:12318948:G:T	H359Q	0.976
19:12319032:G:C	H331Q	0.976
19:12319032:G:T	H331Q	0.976

dbSNP variants (sampled 300 via entrez): RS1000038023 (19:12337734 G>A,C), RS1000062457 (19:12331496 A>G), RS1000111014 (19:12343360 C>G), RS1000127552 (19:12337322 C>T), RS1000478619 (19:12317848 A>T), RS1000508650 (19:12336079 T>TA), RS1000514034 (19:12317663 A>G), RS1000598699 (19:12330567 A>G), RS1000656626 (19:12324418 C>T), RS1000682942 (19:12349032 A>AG), RS1000745243 (19:12318129 A>G), RS1000752312 (19:12330981 A>G), RS1000828463 (19:12323159 G>C), RS1000905347 (19:12347757 A>G), RS1000937230 (19:12330191 A>G)

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

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases mutagenesis	3
dicrotophos	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	affects methylation, increases abundance	1
Nitrogen Dioxide	affects methylation, increases abundance	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1
Particulate Matter	affects methylation, increases abundance	1

Clinical trials (associated diseases)

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