ZNF555

Summary

ZNF555 (zinc finger protein 555, HGNC:28382) is a protein-coding gene on chromosome 19p13.3, encoding Zinc finger protein 555 (Q8NEP9). 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 148254 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_152791

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28382
Approved symbol	ZNF555
Name	zinc finger protein 555
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC26707
Ensembl gene	ENSG00000186300
Ensembl biotype	protein_coding
Entrez	148254

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000334241, ENST00000585966, ENST00000591539, ENST00000905416, ENST00000940323

RefSeq mRNA: 2 — MANE Select: NM_152791 NM_001172775, NM_152791

CCDS: CCDS12096, CCDS59329

Canonical transcript exons

ENST00000334241 — 4 exons

Exon	Start	End
ENSE00001337612	2851468	2851651
ENSE00001337615	2852380	2860471
ENSE00001337616	2841475	2841575
ENSE00003600807	2850587	2850713

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 92.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0725 / max 81.5612, expressed in 1645 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173128	5.0752	1602
173129	0.9973	616

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amniotic fluid	UBERON:0000173	92.98	gold quality
secondary oocyte	CL:0000655	92.56	gold quality
oocyte	CL:0000023	92.08	gold quality
sperm	CL:0000019	87.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.91	gold quality
buccal mucosa cell	CL:0002336	82.15	gold quality
cortical plate	UBERON:0005343	80.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.46	gold quality
cartilage tissue	UBERON:0002418	78.38	gold quality
ventricular zone	UBERON:0003053	77.40	gold quality
esophagus squamous epithelium	UBERON:0006920	77.18	gold quality
ganglionic eminence	UBERON:0004023	76.01	gold quality
islet of Langerhans	UBERON:0000006	75.17	gold quality
corpus callosum	UBERON:0002336	74.13	gold quality
stromal cell of endometrium	CL:0002255	73.92	gold quality
adrenal tissue	UBERON:0018303	72.80	gold quality
calcaneal tendon	UBERON:0003701	72.77	gold quality
endometrium	UBERON:0001295	72.61	gold quality
medial globus pallidus	UBERON:0002477	72.25	gold quality
lower esophagus mucosa	UBERON:0035834	72.20	gold quality
leukocyte	CL:0000738	71.77	gold quality
monocyte	CL:0000576	71.59	gold quality
left ovary	UBERON:0002119	71.35	gold quality
ovary	UBERON:0000992	71.27	gold quality
heart left ventricle	UBERON:0002084	70.93	gold quality
cardiac ventricle	UBERON:0002082	70.87	gold quality
globus pallidus	UBERON:0001875	70.72	gold quality
smooth muscle tissue	UBERON:0001135	70.62	gold quality
uterus	UBERON:0000995	70.58	gold quality
hindlimb stylopod muscle	UBERON:0004252	70.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

156 targeting ZNF555, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-4778-3P	99.93	70.40	1818

Literature-anchored findings (GeneRIF, showing 1)

• Identification of ZNF555 as a putative transcriptional factor highly expressed in human primary myoblasts that interacts with the beta-satellite repeats enhancer site and impacts the ANT1 promoter activity in facioscapulohumeral dystrophy myoblasts. (PMID:26184877)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp78	ENSMUSG00000055150
rattus_norvegicus		ENSRNOG00000083797
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), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 555 — Q8NEP9 (reviewed: Q8NEP9)

All UniProt accessions (2): Q8NEP9, K7ENK0

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 (3)

UniProt ID	Names	Canonical?
Q8NEP9-1	1	yes
Q8NEP9-2	2
Q8NEP9-4	3

RefSeq proteins (2): NP_001166246, NP_690004* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352, PF13894

UniProt features (25 total): zinc finger region 15, sequence variant 4, splice variant 3, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEP9-F1	68.78	0.06

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 57 (showing top): ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, PEDRIOLI_MIR31_TARGETS_UP, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, CREB3L4_TARGET_GENES, LHX9_TARGET_GENES, OVOL3_TARGET_GENES, PHF21A_TARGET_GENES, PRKDC_TARGET_GENES, SALL4_TARGET_GENES

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 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), 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	1
transcription by RNA polymerase II	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
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

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF555	SPATA31E1	Q6ZUB1	505
ZNF555	MALRD1	Q5VYJ5	422
ZNF555	CYLC2	Q14093	418
ZNF555	FANK1	Q8TC84	417
ZNF555	ZNF474	Q6S9Z5	393
ZNF555	SPMIP9	Q96LM6	376
ZNF555	SPATA24	Q86W54	376
ZNF555	SPATC1	Q76KD6	370
ZNF555	TRIM28	Q13263	366
ZNF555	MOSPD1	Q9UJG1	358
ZNF555	ZC3H6	P61129	357
ZNF555	CACNA1B	Q00975	353
ZNF555	SPATA3	Q8NHX4	349
ZNF555	DCUN1D5	Q9BTE7	348
ZNF555	CBY2	Q8NA61	325

IntAct

15 interactions, top by confidence:

A	B	Type	Score
CCNDBP1	ZNF555	psi-mi:“MI:0915”(physical association)	0.670
ZNF555	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.670
ZNF555	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
ZNF555	CEP70	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF555	psi-mi:“MI:0915”(physical association)	0.560
CEP70	ZNF555	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF555	HERC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): ZNF555 (Two-hybrid), ZNF555 (Two-hybrid), KRTAP10-7 (Two-hybrid), FAM73A (Affinity Capture-MS), MTCL1 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), ZNF555 (Affinity Capture-RNA), HERC1 (Affinity Capture-MS), FAM73A (Affinity Capture-MS), MTCL1 (Affinity Capture-MS), ZNF555 (Affinity Capture-MS), ZNF555 (Affinity Capture-MS), ZNF555 (Affinity Capture-MS), ZNF555 (Affinity Capture-MS), ZNF555 (Affinity Capture-MS)

ESM2 similar proteins: A2RRD8, A6NHJ4, B4DX44, O75346, P10077, P10755, P15621, P16372, P16373, P51786, P52737, P85977, Q0VGE8, Q14588, Q147U1, Q15928, Q15973, Q2M3X9, Q3KNS6, Q3MIS6, Q494X3, Q5HY98, Q5RBQ3, Q5REK1, Q5VIY5, Q60585, Q61751, Q6GQR8, Q7L2R6, Q7TSH9, Q8IYX0, Q8N782, Q8N823, Q8N988, Q8N9F8, Q8NA42, Q8NCK3, Q8NDP4, Q8NEP9, 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

660 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2841573:ATGGT:A	donor_loss	1.0000
19:2841574:TGGTG:T	donor_loss	1.0000
19:2841575:GGTG:G	donor_loss	1.0000
19:2841576:G:C	donor_loss	1.0000
19:2850579:T:TA	acceptor_gain	1.0000
19:2850582:TTTA:T	acceptor_loss	1.0000
19:2850583:TTA:T	acceptor_loss	1.0000
19:2850585:A:AG	acceptor_gain	1.0000
19:2850585:A:G	acceptor_loss	1.0000
19:2850585:AG:A	acceptor_gain	1.0000
19:2850586:G:GA	acceptor_gain	1.0000
19:2850586:GG:G	acceptor_gain	1.0000
19:2850709:AGTAG:A	donor_loss	1.0000
19:2850710:GTAG:G	donor_gain	1.0000
19:2850711:TAG:T	donor_gain	1.0000
19:2850714:G:GG	donor_gain	1.0000
19:2850714:GTA:G	donor_loss	1.0000
19:2850715:T:G	donor_loss	1.0000
19:2851459:T:TA	acceptor_gain	1.0000
19:2851466:A:AG	acceptor_gain	1.0000
19:2851467:G:GG	acceptor_gain	1.0000
19:2852379:GTA:G	acceptor_gain	1.0000
19:2841576:G:GG	donor_gain	0.9900
19:2850577:ATT:A	acceptor_gain	0.9900
19:2850583:TTAGG:T	acceptor_gain	0.9900
19:2850584:TAGG:T	acceptor_gain	0.9900
19:2850585:A:T	acceptor_gain	0.9900
19:2850586:G:C	acceptor_gain	0.9900
19:2850586:GGA:G	acceptor_gain	0.9900
19:2850586:GGAC:G	acceptor_gain	0.9900

AlphaMissense

4170 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2852858:T:C	F265L	0.996
19:2852860:C:A	F265L	0.996
19:2852860:C:G	F265L	0.996
19:2852942:T:C	F293L	0.995
19:2852944:T:A	F293L	0.995
19:2852944:T:G	F293L	0.995
19:2853026:T:C	F321L	0.993
19:2853028:C:A	F321L	0.993
19:2853028:C:G	F321L	0.993
19:2852690:T:C	F209L	0.992
19:2852692:T:A	F209L	0.992
19:2852692:T:G	F209L	0.992
19:2853278:T:C	F405L	0.992
19:2853280:C:A	F405L	0.992
19:2853280:C:G	F405L	0.992
19:2852774:T:C	F237L	0.991
19:2852776:T:A	F237L	0.991
19:2852776:T:G	F237L	0.991
19:2853110:T:C	F349L	0.990
19:2853112:C:A	F349L	0.990
19:2853112:C:G	F349L	0.990
19:2853194:T:C	F377L	0.990
19:2853196:C:A	F377L	0.990
19:2853196:C:G	F377L	0.990
19:2853362:T:C	F433L	0.990
19:2853364:C:A	F433L	0.990
19:2853364:C:G	F433L	0.990
19:2852715:G:C	R217P	0.989
19:2853446:T:C	F461L	0.988
19:2853448:C:A	F461L	0.988

dbSNP variants (sampled 300 via entrez): RS1000217973 (19:2849236 C>T), RS1000291602 (19:2849025 G>C), RS1000318270 (19:2843256 T>G), RS1000387075 (19:2856166 T>C), RS1000464593 (19:2844310 C>G,T), RS1000578112 (19:2860944 G>T), RS1000623978 (19:2840275 A>G), RS1000736240 (19:2860638 T>G), RS1000794461 (19:2851511 G>C), RS1000830284 (19:2841775 T>C), RS1001075682 (19:2845777 T>C), RS1001301210 (19:2850323 C>T), RS1001402534 (19:2846073 C>T), RS1001498567 (19:2848832 A>C), RS1001653640 (19:2855211 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

1 associations (top):

Study	Trait	p-value
GCST003518_101	Daytime sleep phenotypes	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement

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
Valproic Acid	affects cotreatment, decreases expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cadmium Chloride	increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
vanadyl sulfate	decreases expression	1
diethyl malate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Azathioprine	increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Ozone	affects expression, increases abundance	1
Phthalic Acids	increases methylation	1
Quercetin	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	increases expression	1
Copper Sulfate	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XW63	HEK293 eGFP-ZNF555	Transformed cell line	Female

Clinical trials (associated diseases)

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