ZNF552

Summary

ZNF552 (zinc finger protein 552, HGNC:26135) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 552 (Q9H707). 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 79818 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_024762

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26135
Approved symbol	ZNF552
Name	zinc finger protein 552
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21603
Ensembl gene	ENSG00000178935
Ensembl biotype	protein_coding
Entrez	79818

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000391701, ENST00000594473, ENST00000596248, ENST00000600397

RefSeq mRNA: 1 — MANE Select: NM_024762 NM_024762

CCDS: CCDS12963

Canonical transcript exons

ENST00000391701 — 3 exons

Exon	Start	End
ENSE00001509501	57807082	57809103
ENSE00003628553	57814711	57814913
ENSE00003630572	57813294	57813420

Expression profiles

Bgee: expression breadth ubiquitous, 211 present calls, max score 97.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0825 / max 58.6409, expressed in 1562 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182915	3.0917	1374
182914	1.9908	987

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.32	gold quality
minor salivary gland	UBERON:0001830	87.02	gold quality
secondary oocyte	CL:0000655	86.08	gold quality
diaphragm	UBERON:0001103	85.91	gold quality
colonic epithelium	UBERON:0000397	85.49	gold quality
mucosa of urinary bladder	UBERON:0001259	85.23	silver quality
body of stomach	UBERON:0001161	84.46	gold quality
olfactory bulb	UBERON:0002264	84.37	silver quality
rectum	UBERON:0001052	84.13	gold quality
mouth mucosa	UBERON:0003729	84.06	gold quality
blood	UBERON:0000178	83.74	gold quality
saliva-secreting gland	UBERON:0001044	83.28	gold quality
stomach	UBERON:0000945	83.24	gold quality
prostate gland	UBERON:0002367	82.35	gold quality
oocyte	CL:0000023	82.23	gold quality
type B pancreatic cell	CL:0000169	82.22	gold quality
mucosa of transverse colon	UBERON:0004991	81.97	gold quality
urinary bladder	UBERON:0001255	81.68	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	81.60	gold quality
amniotic fluid	UBERON:0000173	81.20	silver quality
gall bladder	UBERON:0002110	80.55	gold quality
mammary duct	UBERON:0001765	80.44	gold quality
sural nerve	UBERON:0015488	80.23	gold quality
epithelium of mammary gland	UBERON:0003244	80.05	gold quality
transverse colon	UBERON:0001157	79.97	gold quality
bone marrow cell	CL:0002092	79.84	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.27	gold quality
vagina	UBERON:0000996	78.98	gold quality
adrenal tissue	UBERON:0018303	78.87	gold quality
epithelium of nasopharynx	UBERON:0001951	78.66	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.80
E-MTAB-6142	no	76.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting ZNF552, 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-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-3164	99.02	68.39	1071

Literature-anchored findings (GeneRIF, showing 1)

• ZNF552 was a transcriptional repressor, and overexpression of ZNF552 in the COS-7 cells inhibited the transcriptional activities of AP-1 and SRE, which could be relieved through RNAi analysis. (PMID:20356460)

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), 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), 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 552 — Q9H707 (reviewed: Q9H707)

All UniProt accessions (3): Q9H707, M0QZ81, M0R2C3

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_079038* (*=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 9, cross-link 5, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H707-F1	59.28	0.19

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 176, 198, 251, 266, 308

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 49 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, GREB1_TARGET_GENES, H1_6_TARGET_GENES, HOXC6_TARGET_GENES, PRKDC_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR4729, MIR6508_5P

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

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF552	ZNF232	Q9UNY5	404
ZNF552	ZNF521	Q96K83	396
ZNF552	FAM234B	A2RU67	393
ZNF552	ZNF148	Q9UQR1	392
ZNF552	ZNF853	P0CG23	382
ZNF552	NIF3L1	Q9GZT8	370
ZNF552	MSH6	P52701	353
ZNF552	MSH3	P20585	353
ZNF552	EPHB2	P29323	353
ZNF552	CPPED1	Q9BRF8	325
ZNF552	DCAF5	Q96JK2	324
ZNF552	NKAIN1	Q4KMZ8	324
ZNF552	SERTAD3	Q9UJW9	323
ZNF552	H2AC7	P20671	315
ZNF552	CREBL2	O60519	300

IntAct

116 interactions, top by confidence:

A	B	Type	Score
PHF24	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
CARD10	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-5	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
CCNDBP1	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
TP53BP2	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF837	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF552	ZRANB1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-11	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF552	MID2	psi-mi:“MI:0915”(physical association)	0.560
GYS1	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF552	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
KCTD7	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF648	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
SCNM1	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
DVL3	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF792	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZNF552	PHF24	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
TEKT4	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
ZBTB16	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
AP1M1	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
GEM	ZNF552	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (45): ZNF552 (Affinity Capture-MS), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid), ZNF552 (Two-hybrid)

ESM2 similar proteins: A0A2K5V015, A1YIY0, A8MUZ8, A8MWA4, B8JI71, O08569, P01133, P0DJ43, P14370, P14585, P17630, P19070, P48357, P82279, P97435, Q07444, Q0D2K5, Q28066, Q28660, Q29RU2, Q4KUS1, Q5G872, Q5R6R1, Q5RCW9, Q5T1H1, Q5UKY4, Q5Z5Q3, Q60736, Q63515, Q63722, Q6DFV8, Q6GMZ9, Q6V0K7, Q6ZN79, Q7TSY4, Q811Q4, Q8N2E2, Q8VHS2, Q90Y54, Q95MI4

Diamond homologs: A2VDP4, B7Z6K7, D3ZVT0, E7ETH6, E9Q8G5, O43296, O43361, O75290, O75467, O75820, P0CH99, P0CI00, P15621, P17021, P17023, P17024, P17030, P17032, P52740, P52741, Q02525, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q13106, Q13398, Q14587, Q147U1, Q15935, Q2M218, Q2M3X9, Q32M78, Q3KQV3, Q3SY52, Q3V080, Q3ZCX4, Q4R882, Q4V8A8, Q5CZA5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

321 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
19:57813286: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
19:57813429:A:C	acceptor_gain	0.9700
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
19:57813293:CCCA:C	donor_gain	0.9500
19:57813418:GCCC:G	acceptor_loss	0.9500
19:57813421:C:A	acceptor_loss	0.9500
19:57813421:C:CC	acceptor_gain	0.9500
19:57813422:T:A	acceptor_loss	0.9500
19:57814837:T:TA	donor_gain	0.9500
19:57809101:AACC:A	acceptor_loss	0.9400
19:57809102:ACCT:A	acceptor_loss	0.9400
19:57809103:CCTGA:C	acceptor_loss	0.9400

AlphaMissense

2721 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57808181:A:C	F361L	0.998
19:57808181:A:T	F361L	0.998
19:57808183:A:G	F361L	0.998
19:57808265:A:C	F333L	0.997
19:57808265:A:T	F333L	0.997
19:57808267:A:G	F333L	0.997
19:57808097:A:C	F389L	0.995
19:57808097:A:T	F389L	0.995
19:57808099:A:G	F389L	0.995
19:57808164:A:G	L367P	0.992
19:57808154:G:C	H370Q	0.991
19:57808154:G:T	H370Q	0.991
19:57808182:A:G	F361S	0.991
19:57808320:T:G	Q315P	0.991
19:57808322:G:C	H314Q	0.990
19:57808322:G:T	H314Q	0.990
19:57808349:A:C	F305L	0.990
19:57808349:A:T	F305L	0.990
19:57808351:A:G	F305L	0.990
19:57808156:G:C	H370D	0.989
19:57808240:G:C	H342D	0.989
19:57808310:G:C	H318Q	0.989
19:57808310:G:T	H318Q	0.989
19:57808266:A:G	F333S	0.988
19:57808324:G:C	H314D	0.988
19:57808332:A:G	L311P	0.987
19:57808142:G:C	H374Q	0.986
19:57808142:G:T	H374Q	0.986
19:57813385:A:C	F23L	0.985
19:57813385:A:T	F23L	0.985

dbSNP variants (sampled 300 via entrez): RS1000044255 (19:57816906 A>G), RS1000739033 (19:57807507 A>G), RS1001139705 (19:57813744 T>A,C), RS1001299009 (19:57813596 T>C), RS1001807437 (19:57811137 C>A,G,T), RS1001970313 (19:57811026 C>T), RS1002081221 (19:57806868 G>A), RS1002637280 (19:57813818 C>T), RS1003237044 (19:57809647 A>T), RS1003256247 (19:57815414 A>G), RS1003642492 (19:57815089 G>A), RS1003781530 (19:57813965 A>C), RS1004155189 (19:57809661 T>A), RS1004918120 (19:57814528 T>C), RS1004930970 (19:57814156 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

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	3
Air Pollutants	increases expression, decreases expression, increases abundance	2
Doxorubicin	decreases expression, affects cotreatment, affects response to substance	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
resorcinol	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases expression	1
Cyclophosphamide	affects cotreatment, affects response to substance	1
Fluorouracil	affects cotreatment, affects response to substance	1
Methylcholanthrene	affects binding, increases reaction	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Rotenone	decreases expression	1
Selenium	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases expression	1
Paclitaxel	affects cotreatment, affects response to substance	1
Lactic Acid	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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