ZNF550

Summary

ZNF550 (zinc finger protein 550, HGNC:28643) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 550 (Q7Z398). 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 162972 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001397372

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28643
Approved symbol	ZNF550
Name	zinc finger protein 550
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	MGC41917
Ensembl gene	ENSG00000251369
Ensembl biotype	protein_coding
Entrez	162972

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 nonsense_mediated_decay, 3 protein_coding, 1 retained_intron

ENST00000344222, ENST00000376230, ENST00000447310, ENST00000457177, ENST00000506609, ENST00000595560, ENST00000601415, ENST00000699333

RefSeq mRNA: 5 — MANE Select: NM_001397372 NM_001277090, NM_001277091, NM_001277092, NM_001277093, NM_001397372

CCDS: CCDS35500

Canonical transcript exons

ENST00000699333 — 4 exons

Exon	Start	End
ENSE00001678372	57559656	57559863
ENSE00003064890	57556231	57556357
ENSE00003113217	57552627	57552722
ENSE00003976281	57541838	57547993

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 94.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.7631 / max 96.2539, expressed in 1509 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182909	2.8754	1261
182908	1.8877	973

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	94.25	gold quality
germinal epithelium of ovary	UBERON:0001304	85.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.61	gold quality
tibia	UBERON:0000979	82.08	gold quality
cortical plate	UBERON:0005343	81.48	gold quality
ventricular zone	UBERON:0003053	81.00	gold quality
Brodmann (1909) area 23	UBERON:0013554	80.83	gold quality
epithelium of nasopharynx	UBERON:0001951	80.28	gold quality
ganglionic eminence	UBERON:0004023	80.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.57	gold quality
ovary	UBERON:0000992	78.92	gold quality
lymph node	UBERON:0000029	78.87	gold quality
calcaneal tendon	UBERON:0003701	78.42	gold quality
granulocyte	CL:0000094	78.17	gold quality
stromal cell of endometrium	CL:0002255	78.17	gold quality
left ovary	UBERON:0002119	77.95	gold quality
apex of heart	UBERON:0002098	77.12	gold quality
spleen	UBERON:0002106	76.97	gold quality
right ovary	UBERON:0002118	76.94	gold quality
heart left ventricle	UBERON:0002084	76.77	gold quality
cardiac ventricle	UBERON:0002082	76.58	gold quality
tonsil	UBERON:0002372	76.31	gold quality
upper leg skin	UBERON:0004262	76.28	gold quality
colonic epithelium	UBERON:0000397	76.25	gold quality
adrenal tissue	UBERON:0018303	76.12	gold quality
cerebellar cortex	UBERON:0002129	76.10	gold quality
cerebellar hemisphere	UBERON:0002245	76.07	gold quality
skin of leg	UBERON:0001511	76.03	gold quality
pituitary gland	UBERON:0000007	76.00	gold quality
endometrium	UBERON:0001295	76.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.75

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300)

Protein

Protein identifiers

Zinc finger protein 550 — Q7Z398 (reviewed: Q7Z398)

All UniProt accessions (4): A0A0C4DGB4, Q7Z398, M0QWZ8, M0R337

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?
Q7Z398-1	1	yes
Q7Z398-2	2

RefSeq proteins (5): NP_001264019, NP_001264020, NP_001264021, NP_001264022, NP_001384301* (*=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 (15 total): zinc finger region 8, chain 1, domain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z398-F1	67.30	0.25

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 59 (showing top): BIDUS_METASTASIS_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PRC2_SUZ12_UP.V1_UP, IL21_UP.V1_DN, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, JAK2_DN.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, ZNF8_TARGET_GENES, ZNF92_TARGET_GENES, MIR95_5P

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892), 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
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
DNA-templated transcription	2
regulation of transcription by RNA polymerase II	2
negative regulation of RNA biosynthetic process	1
positive regulation of 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

628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF550	OR2A2	Q6IF42	590
ZNF550	FREY1	C9JXX5	541
ZNF550	U2SURP	O15042	437
ZNF550	PPP1R14D	Q9NXH3	428
ZNF550	UBTD1	Q9HAC8	400
ZNF550	ERVMER34-1	Q9H9K5	394
ZNF550	SYPL1	Q16563	359
ZNF550	UTP15	Q8TED0	357
ZNF550	NAPG	Q99747	333
ZNF550	GPAA1	O43292	324
ZNF550	PPP2R3C	Q969Q6	311
ZNF550	NCKIPSD	Q9NZQ3	308
ZNF550	RABGAP1L	Q5R372	302
ZNF550	CREBRF	Q8IUR6	299
ZNF550	DNAH3	Q8TD57	290

IntAct

10 interactions, top by confidence:

A	B	Type	Score
ZNF550	REL	psi-mi:“MI:0915”(physical association)	0.560
ZNF550	MDM2	psi-mi:“MI:0914”(association)	0.530
ZNF550	MEIOC	psi-mi:“MI:0914”(association)	0.350
NOL4	ZNF195	psi-mi:“MI:0914”(association)	0.350
ZNF550	A2ML1	psi-mi:“MI:0914”(association)	0.350
SLC27A4	IPO5	psi-mi:“MI:0914”(association)	0.350

BioGRID (97): ZNF550 (Two-hybrid), C17orf104 (Affinity Capture-MS), ZNF714 (Affinity Capture-MS), YTHDC2 (Affinity Capture-MS), TRIM37 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF92 (Affinity Capture-MS), RBAK (Affinity Capture-MS), USP34 (Affinity Capture-MS), TRIM41 (Affinity Capture-MS), FBLN5 (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), STRN4 (Affinity Capture-MS), PPP2R1B (Affinity Capture-MS), STRN3 (Affinity Capture-MS)

ESM2 similar proteins: A2A761, A2T7D2, A3KN32, A3KN36, A7MBI1, B2RXC5, E9PYI1, O43296, P0CG31, P10072, P10078, P17023, P17097, P18725, P18728, P52738, Q02525, Q07231, Q0VCB0, Q12901, Q14592, Q49AA0, Q4V8A8, Q571J5, Q5CZA5, Q5JNZ3, Q5R7I8, Q5RB33, Q5RBX0, Q5RBY9, Q61967, Q62396, Q6PF04, Q6ZNG0, Q6ZS27, Q7Z398, Q80YP6, Q8BIQ3, Q8IZ26, Q96N20

Diamond homologs: A0JPL0, A2A761, A3KN32, A3KN36, A6NFI3, A6NM28, A6QLU5, A6QPT6, A7MBI1, A8MTY0, B2RXC5, B4DU55, E9PYI1, O14978, O60765, O75467, O75820, O95780, P0C7X2, P0DKX0, P0DPD5, P10072, P15622, P16374, P17014, P17023, P17032, P17098, P51523, P51786, P52738, P52742, Q02975, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q14590, Q14929, Q29RZ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1032 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57556225:CATTA:C	donor_loss	1.0000
19:57556226:ATTAC:A	donor_loss	1.0000
19:57556228:TACC:T	donor_loss	1.0000
19:57556229:A:C	donor_loss	1.0000
19:57556353:AACAT:A	acceptor_gain	1.0000
19:57556354:ACAT:A	acceptor_gain	1.0000
19:57556355:CAT:C	acceptor_gain	1.0000
19:57556355:CATC:C	acceptor_gain	1.0000
19:57556356:AT:A	acceptor_gain	1.0000
19:57556356:ATCTG:A	acceptor_loss	1.0000
19:57556358:C:CC	acceptor_gain	1.0000
19:57556358:CT:C	acceptor_loss	1.0000
19:57559651:CTCA:C	donor_loss	1.0000
19:57559652:TCA:T	donor_loss	1.0000
19:57559653:CA:C	donor_loss	1.0000
19:57559655:C:CT	donor_loss	1.0000
19:57544457:AGGG:A	donor_gain	0.9900
19:57544503:T:TA	donor_gain	0.9900
19:57552621:GCTTA:G	donor_loss	0.9900
19:57552622:CTTA:C	donor_loss	0.9900
19:57552624:TACCT:T	donor_loss	0.9900
19:57552625:A:AT	donor_loss	0.9900
19:57552719:TGCC:T	acceptor_gain	0.9900
19:57556359:T:A	acceptor_loss	0.9900
19:57556367:C:CT	acceptor_gain	0.9900
19:57559650:GCTCA:G	donor_loss	0.9900
19:57559654:A:AC	donor_gain	0.9900
19:57559655:C:CC	donor_gain	0.9900
19:57552719:TGCCC:T	acceptor_loss	0.9800
19:57552720:GCCCT:G	acceptor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000003470 (19:57553769 G>A), RS1000183925 (19:57545838 C>G,T), RS1000231384 (19:57545537 G>GAC), RS1000239305 (19:57553555 T>A,C), RS1000344498 (19:57551556 T>C), RS1000473403 (19:57558441 A>G), RS1000555832 (19:57547319 G>A,C), RS1000626422 (19:57559826 C>A,T), RS1000630023 (19:57553719 A>T), RS1000696817 (19:57552107 G>A,T), RS1000806527 (19:57559823 GC>G), RS1000880706 (19:57542303 T>C), RS1000957664 (19:57555237 A>G), RS1001157429 (19:57548348 G>T), RS1001232206 (19:57548577 C>A)

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

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

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
terbufos	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
cupric oxide	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
pentabromodiphenyl ether	increases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Fonofos	increases methylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gallic Acid	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Parathion	increases methylation	1
Phenobarbital	affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Zinc	decreases expression	1
Aflatoxin B1	increases methylation	1
Gold Compounds	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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