ZNF548

Summary

ZNF548 (zinc finger protein 548, HGNC:26561) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 548 (Q8NEK5). 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 147694 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_001172773

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26561
Approved symbol	ZNF548
Name	zinc finger protein 548
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32932
Ensembl gene	ENSG00000188785
Ensembl biotype	protein_coding
Entrez	147694

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron

ENST00000336128, ENST00000366197, ENST00000594668, ENST00000594693, ENST00000596282, ENST00000597047, ENST00000597400, ENST00000597576, ENST00000598895, ENST00000600442, ENST00000600927, ENST00000602086

RefSeq mRNA: 2 — MANE Select: NM_001172773 NM_001172773, NM_152909

CCDS: CCDS46209, CCDS54324

Canonical transcript exons

ENST00000336128 — 4 exons

Exon	Start	End
ENSE00003055153	57389854	57390114
ENSE00003534399	57397048	57397174
ENSE00003552707	57394188	57394223
ENSE00004282245	57398430	57402992

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 97.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2758 / max 128.3385, expressed in 1761 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177770	7.2927	1713
177771	2.9831	975

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	97.69	gold quality
buccal mucosa cell	CL:0002336	96.55	gold quality
superficial temporal artery	UBERON:0001614	96.33	gold quality
gingiva	UBERON:0001828	95.11	gold quality
germinal epithelium of ovary	UBERON:0001304	93.43	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.38	gold quality
cardia of stomach	UBERON:0001162	93.07	gold quality
lower lobe of lung	UBERON:0008949	89.44	gold quality
subthalamic nucleus	UBERON:0001906	88.06	gold quality
lateral globus pallidus	UBERON:0002476	87.28	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.81	gold quality
ventral tegmental area	UBERON:0002691	86.49	gold quality
secondary oocyte	CL:0000655	86.33	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	86.24	gold quality
biceps brachii	UBERON:0001507	85.96	gold quality
vena cava	UBERON:0004087	85.73	gold quality
cauda epididymis	UBERON:0004360	85.34	gold quality
upper leg skin	UBERON:0004262	85.25	gold quality
heart right ventricle	UBERON:0002080	85.16	gold quality
lymph node	UBERON:0000029	85.15	gold quality
tonsil	UBERON:0002372	84.88	gold quality
colonic epithelium	UBERON:0000397	84.81	gold quality
body of tongue	UBERON:0011876	84.75	gold quality
superior vestibular nucleus	UBERON:0007227	84.55	gold quality
superior surface of tongue	UBERON:0007371	84.51	gold quality
omental fat pad	UBERON:0010414	84.49	gold quality
peritoneum	UBERON:0002358	84.46	gold quality
mammary duct	UBERON:0001765	84.43	gold quality
substantia nigra pars reticulata	UBERON:0001966	84.39	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.35	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

130 targeting ZNF548, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562

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), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 548 — Q8NEK5 (reviewed: Q8NEK5)

All UniProt accessions (10): Q8NEK5, M0QX17, M0QXE2, M0QY53, M0QYA3, M0R041, M0R1K1, M0R2J6, M0R354, M0R3F2

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?
Q8NEK5-1	1	yes
Q8NEK5-2	2

RefSeq proteins (2): NP_001166244, NP_690873 (=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
IPR050527

Pfam: PF00096, PF01352

UniProt features (18 total): zinc finger region 11, sequence variant 2, chain 1, domain 1, cross-link 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEK5-F1	67.04	0.32

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): 516

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 59 (showing top): WANG_CLIM2_TARGETS_UP, PEREZ_TP63_TARGETS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FEVR_CTNNB1_TARGETS_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, UBN1_TARGET_GENES, ZFP91_TARGET_GENES, ZNF577_TARGET_GENES, MIR5688, MIR495_3P, MIR4728_5P, MIR15A_5P, MIR195_5P, MIR15B_5P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): 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), 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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

412 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF548	ZNF385B	Q569K4	561
ZNF548	TSHZ3	Q63HK5	456
ZNF548	YIF1A	O95070	368
ZNF548	APMAP	Q9HDC9	360
ZNF548	MYG1	Q9HB07	352
ZNF548	DDX19A	Q9NUU7	349
ZNF548	BCAP29	Q9UHQ4	336
ZNF548	CWF19L2	Q2TBE0	320
ZNF548	USP33	Q8TEY7	317
ZNF548	POGZ	Q7Z3K3	308
ZNF548	PFDN5	Q99471	305
ZNF548	ANAPC7	Q9UJX3	305
ZNF548	PRKAB2	O43741	294
ZNF548	TTK	P33981	290
ZNF548	CSTF1	Q05048	287

IntAct

4 interactions, top by confidence:

A	B	Type	Score
LRRC36	TBL1X	psi-mi:“MI:0914”(association)	0.350
DISC1	ZNF548	psi-mi:“MI:0915”(physical association)	0.000
NDEL1	ZNF548	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZNF548 (Affinity Capture-MS), ZNF548 (Affinity Capture-MS), ZNF548 (Affinity Capture-MS), ZNF548 (Affinity Capture-MS), ZNF548 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1141 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57390704:T:A	acceptor_gain	1.0000
19:57397038:A:AG	acceptor_gain	1.0000
19:57390001:G:GG	donor_gain	0.9900
19:57390110:CTGAG:C	donor_loss	0.9900
19:57390111:TGAGG:T	donor_loss	0.9900
19:57390115:G:GA	donor_loss	0.9900
19:57390116:T:A	donor_loss	0.9900
19:57394186:AG:A	acceptor_gain	0.9900
19:57394187:GG:G	acceptor_gain	0.9900
19:57397038:AATTT:A	acceptor_gain	0.9900
19:57397039:A:G	acceptor_gain	0.9900
19:57397042:T:TA	acceptor_gain	0.9900
19:57397042:TGGCA:T	acceptor_loss	0.9900
19:57397043:G:A	acceptor_gain	0.9900
19:57397045:CA:C	acceptor_loss	0.9900
19:57397046:A:AG	acceptor_gain	0.9900
19:57397046:A:T	acceptor_loss	0.9900
19:57397046:AG:A	acceptor_gain	0.9900
19:57397047:G:GG	acceptor_gain	0.9900
19:57397047:GG:G	acceptor_gain	0.9900
19:57397047:GGGCC:G	acceptor_gain	0.9900
19:57397173:AGGT:A	donor_loss	0.9900
19:57397173:AGGTA:A	donor_loss	0.9900
19:57397174:GGT:G	donor_loss	0.9900
19:57397176:TAA:T	donor_loss	0.9900
19:57389998:GGA:G	donor_gain	0.9800
19:57389999:GAG:G	donor_gain	0.9800
19:57394222:AGGT:A	donor_loss	0.9800
19:57394222:AGGTG:A	donor_loss	0.9800
19:57394224:G:A	donor_loss	0.9800

AlphaMissense

3664 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57399659:T:C	F458L	0.999
19:57399661:T:A	F458L	0.999
19:57399661:T:G	F458L	0.999
19:57399594:T:C	L436P	0.997
19:57399743:T:C	F486L	0.997
19:57399745:T:A	F486L	0.997
19:57399745:T:G	F486L	0.997
19:57399575:T:C	F430L	0.995
19:57399577:T:A	F430L	0.995
19:57399577:T:G	F430L	0.995
19:57399604:T:A	H439Q	0.995
19:57399604:T:G	H439Q	0.995
19:57399616:C:A	H443Q	0.995
19:57399616:C:G	H443Q	0.995
19:57399491:T:C	F402L	0.994
19:57399493:T:A	F402L	0.994
19:57399493:T:G	F402L	0.994
19:57399660:T:C	F458S	0.994
19:57399520:C:A	H411Q	0.993
19:57399520:C:G	H411Q	0.993
19:57399678:T:C	L464P	0.993
19:57399688:C:A	H467Q	0.993
19:57399688:C:G	H467Q	0.993
19:57399690:A:C	Q468P	0.993
19:57399762:T:C	L492P	0.993
19:57399602:C:G	H439D	0.992
19:57399610:A:C	R441S	0.992
19:57399610:A:T	R441S	0.992
19:57399629:C:T	P448S	0.991
19:57399686:C:G	H467D	0.991

dbSNP variants (sampled 300 via entrez): RS1000012483 (19:57394534 A>G), RS1000246240 (19:57401155 T>G), RS1000289195 (19:57393894 T>C), RS1000591951 (19:57400726 C>T), RS1000979745 (19:57389973 G>A), RS1000993457 (19:57389041 A>G), RS1001032452 (19:57391355 C>T), RS1001090888 (19:57396394 G>A), RS1001264904 (19:57389793 A>G), RS1001341831 (19:57395164 T>C), RS1001698991 (19:57393003 C>T), RS1001785626 (19:57393397 A>C), RS1002131656 (19:57400676 G>A), RS1002340005 (19:57399839 C>G), RS1002396580 (19:57394570 G>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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
sodium arsenite	decreases expression, increases abundance, increases expression	3
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Coal	decreases expression, increases abundance	1
Dieldrin	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression, increases abundance	1
Tobacco Smoke Pollution	increases expression	1
Antirheumatic Agents	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_XW62	HEK293 eGFP-ZNF548	Transformed cell line	Female

Clinical trials (associated diseases)

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