ZNF554

Summary

ZNF554 (zinc finger protein 554, HGNC:26629) is a protein-coding gene on chromosome 19p13.3, encoding Zinc finger protein 554 (Q86TJ5). 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. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 115196 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_001102651

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26629
Approved symbol	ZNF554
Name	zinc finger protein 554
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34817
Ensembl gene	ENSG00000172006
Ensembl biotype	protein_coding
Entrez	115196

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000317243, ENST00000588534, ENST00000590116, ENST00000591265, ENST00000901630, ENST00000963470, ENST00000963471

RefSeq mRNA: 1 — MANE Select: NM_001102651 NM_001102651

CCDS: CCDS42462

Canonical transcript exons

ENST00000317243 — 5 exons

Exon	Start	End
ENSE00001387977	2823040	2823112
ENSE00001391742	2819868	2820124
ENSE00002758110	2833681	2836735
ENSE00003507607	2827617	2827743
ENSE00003573550	2832303	2832494

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 97.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.5300 / max 43.4608, expressed in 1497 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173126	2.7796	1420
173127	0.7504	401

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.79	gold quality
endothelial cell	CL:0000115	94.65	gold quality
amniotic fluid	UBERON:0000173	93.33	gold quality
tendon of biceps brachii	UBERON:0008188	89.35	silver quality
secondary oocyte	CL:0000655	85.51	gold quality
oocyte	CL:0000023	84.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.37	gold quality
medial globus pallidus	UBERON:0002477	82.63	gold quality
cardiac muscle of right atrium	UBERON:0003379	81.89	gold quality
left ventricle myocardium	UBERON:0006566	81.88	gold quality
Brodmann (1909) area 23	UBERON:0013554	81.86	gold quality
placenta	UBERON:0001987	80.70	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.67	gold quality
globus pallidus	UBERON:0001875	79.79	silver quality
esophagus squamous epithelium	UBERON:0006920	79.62	silver quality
pancreatic ductal cell	CL:0002079	79.49	silver quality
cortical plate	UBERON:0005343	79.31	gold quality
middle temporal gyrus	UBERON:0002771	79.21	silver quality
prefrontal cortex	UBERON:0000451	77.27	gold quality
upper arm skin	UBERON:0004263	77.12	gold quality
primary visual cortex	UBERON:0002436	76.94	gold quality
gastrocnemius	UBERON:0001388	76.18	gold quality
muscle of leg	UBERON:0001383	75.90	gold quality
cerebellar cortex	UBERON:0002129	75.70	gold quality
cerebellar hemisphere	UBERON:0002245	75.65	gold quality
frontal cortex	UBERON:0001870	75.62	gold quality
neocortex	UBERON:0001950	75.43	gold quality
cerebellum	UBERON:0002037	75.36	gold quality
right frontal lobe	UBERON:0002810	75.31	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.81
E-GEOD-81608	no	7.49

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Decreased Expression of ZNF554 in Gliomas is Associated with the Activation of Tumor Pathways and Shorter Patient Survival. (PMID:32796700)
• Dysfunction of ZNF554 promotes ROS-induced apoptosis and autophagy in Fetal Growth Restriction via the p62-Keap1-Nrf2 pathway. (PMID:37804692)
• ZNF554 Inhibits Endometrial Cancer Progression via Regulating RBM5 and Inactivating WNT/beta-Catenin Signaling Pathway. (PMID:38619681)

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), 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), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 554 — Q86TJ5 (reviewed: Q86TJ5)

All UniProt accessions (3): Q86TJ5, K7EIR8, K7EQV8

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_001096121* (*=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
IPR050888	ZnF_C2H2-type_TF	Family

Pfam: PF00096, PF01352, PF13465

UniProt features (13 total): zinc finger region 8, sequence variant 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86TJ5-F1	56.22	0.23

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 (1): 178

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 54 (showing top): GOCC_NUCLEOLUS, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, KUMAR_AUTOPHAGY_NETWORK, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CBX7_TARGET_GENES, DACH1_TARGET_GENES, HMG20B_TARGET_GENES, HMGA1_TARGET_GENES, SNIP1_TARGET_GENES, TOP2B_TARGET_GENES, WDHD1_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF146_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 (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

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
nuclear lumen	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
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
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF554	MYADM	Q96S97	477
ZNF554	MALRD1	Q5VYJ5	413
ZNF554	FANK1	Q8TC84	409
ZNF554	TAFA2	Q8N3H0	382
ZNF554	ZNF474	Q6S9Z5	370
ZNF554	DHRS13	Q6UX07	359
ZNF554	CACNA1B	Q00975	353
ZNF554	AMDHD1	Q96NU7	345
ZNF554	STK40	Q8N2I9	308
ZNF554	ZMAT1	Q5H9K5	297
ZNF554	TRIM28	Q13263	292
ZNF554	PCNX1	Q96RV3	270
ZNF554	MYT1	Q01538	256
ZNF554	HMCES	Q96FZ2	248
ZNF554	LGALS14	Q8TCE9	246

IntAct

14 interactions, top by confidence:

A	B	Type	Score
ZNF554	TSEN15	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	ZNF554	psi-mi:“MI:0915”(physical association)	0.560
ZNF554		psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
COPS5	FBLL1	psi-mi:“MI:0914”(association)	0.350
MVD	FASN	psi-mi:“MI:0914”(association)	0.350
ZNF554	TRIM37	psi-mi:“MI:0914”(association)	0.350
TSEN15	ZNF554	psi-mi:“MI:0915”(physical association)	0.000
POLR1C	ZNF554	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): ZNF554 (Two-hybrid), TSEN15 (Two-hybrid), STK3 (Affinity Capture-MS), STK4 (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), ZNF808 (Affinity Capture-MS), SAV1 (Affinity Capture-MS), TRIM37 (Affinity Capture-MS), ZNF554 (Affinity Capture-MS), ZNF554 (Affinity Capture-MS), ZNF554 (Affinity Capture-MS), ZNF554 (Affinity Capture-RNA), ZNF554 (Affinity Capture-MS)

ESM2 similar proteins: A0JPL0, A1L1L7, A7MBI1, A8MT65, B2RXC5, G3X9G7, P0CG31, P21506, P52738, Q02525, Q2KI58, Q2M3W8, Q49AA0, Q4R6J4, Q5FWF6, Q5RB33, Q5RCJ2, Q5RE50, Q5REF1, Q5T5D7, Q5VIY5, Q6V9R5, Q6ZMW2, Q6ZN11, Q6ZNG0, Q86TJ5, Q86XU0, Q8BGV5, Q8N782, Q8N859, Q8N883, Q8N9Z0, Q8NC26, Q8NE65, Q95K49, Q96N20, Q96NG8, Q96NJ3, Q96SR6, Q9BSK1

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1199 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2820120:CAGCC:C	donor_gain	1.0000
19:2820121:AGCC:A	donor_gain	1.0000
19:2820122:GCC:G	donor_gain	1.0000
19:2820122:GCCG:G	donor_gain	1.0000
19:2820122:GCCGT:G	donor_loss	1.0000
19:2820123:CC:C	donor_gain	1.0000
19:2820123:CCGT:C	donor_loss	1.0000
19:2820124:CGT:C	donor_loss	1.0000
19:2820125:G:GG	donor_gain	1.0000
19:2820126:T:G	donor_loss	1.0000
19:2830476:G:GG	donor_gain	1.0000
19:2820002:G:T	donor_gain	0.9900
19:2820127:AAGT:A	donor_loss	0.9900
19:2832301:A:AG	acceptor_gain	0.9900
19:2832302:G:GG	acceptor_gain	0.9900
19:2833679:A:AG	acceptor_gain	0.9900
19:2833680:G:GG	acceptor_gain	0.9900
19:2827535:T:TA	acceptor_gain	0.9800
19:2827743:GGTAA:G	donor_loss	0.9800
19:2827744:G:GA	donor_loss	0.9800
19:2827745:TAAGG:T	donor_loss	0.9800
19:2832302:GA:G	acceptor_gain	0.9800
19:2832302:GAA:G	acceptor_gain	0.9800
19:2833675:TTTCA:T	acceptor_loss	0.9800
19:2833676:TTCA:T	acceptor_loss	0.9800
19:2833677:TCAG:T	acceptor_loss	0.9800
19:2833678:CAGAT:C	acceptor_loss	0.9800
19:2833679:A:G	acceptor_loss	0.9800
19:2833679:AGATT:A	acceptor_gain	0.9800
19:2833680:G:GC	acceptor_loss	0.9800

AlphaMissense

3557 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2834316:T:C	F361L	0.999
19:2834318:T:A	F361L	0.999
19:2834318:T:G	F361L	0.999
19:2834400:T:C	F389L	0.999
19:2834402:C:A	F389L	0.999
19:2834402:C:G	F389L	0.999
19:2834484:T:C	F417L	0.999
19:2834486:C:A	F417L	0.999
19:2834486:C:G	F417L	0.999
19:2834568:T:C	F445L	0.999
19:2834570:C:A	F445L	0.999
19:2834570:C:G	F445L	0.999
19:2834652:T:C	F473L	0.999
19:2834654:C:A	F473L	0.999
19:2834654:C:G	F473L	0.999
19:2834736:T:C	F501L	0.999
19:2834738:C:A	F501L	0.999
19:2834738:C:G	F501L	0.999
19:2834602:G:C	R456P	0.998
19:2834503:T:C	L423P	0.997
19:2834511:C:G	H426D	0.997
19:2834569:T:C	F445S	0.997
19:2834587:T:C	L451P	0.997
19:2834653:T:C	F473S	0.997
19:2834679:C:G	H482D	0.997
19:2834317:T:C	F361S	0.996
19:2834401:T:C	F389S	0.996
19:2834419:T:C	L395P	0.996
19:2834429:T:A	H398Q	0.996
19:2834429:T:G	H398Q	0.996

dbSNP variants (sampled 300 via entrez): RS1000127411 (19:2823334 G>A,C), RS1000207293 (19:2825404 C>T), RS1000213156 (19:2830831 T>C), RS1000263844 (19:2830584 A>G), RS1000448791 (19:2820145 C>G,T), RS1000809696 (19:2835446 T>C), RS1000893237 (19:2825557 G>A), RS1000989871 (19:2822249 C>G), RS1001258019 (19:2835212 C>T), RS1001566809 (19:2820997 T>A,C), RS1001824450 (19:2830765 A>T), RS1001938835 (19:2829532 G>A), RS1002000319 (19:2820354 G>C,T), RS1002048176 (19:2835848 G>A), RS1002052428 (19:2820225 G>A,T)

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

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	increases expression	2
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
ferrous chloride	decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
(+)-JQ1 compound	increases expression	1
Arsenic Trioxide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Amiodarone	increases expression	1
Azathioprine	increases expression	1
Cadmium	increases expression	1
Drugs, Chinese Herbal	increases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1
Naphthoquinones	increases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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