ZNF524

Summary

ZNF524 (zinc finger protein 524, HGNC:28322) is a protein-coding gene on chromosome 19q13.42, encoding Zinc finger protein 524 (Q96C55). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 147807 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_153219

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28322
Approved symbol	ZNF524
Name	zinc finger protein 524
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	MGC23143
Ensembl gene	ENSG00000171443
Ensembl biotype	protein_coding
Entrez	147807

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000301073, ENST00000589521, ENST00000591046, ENST00000882303, ENST00000882304, ENST00000882305, ENST00000938530, ENST00000972332

RefSeq mRNA: 1 — MANE Select: NM_153219 NM_153219

CCDS: CCDS12929

Canonical transcript exons

ENST00000301073 — 2 exons

Exon	Start	End
ENSE00001114248	55602075	55603138
ENSE00001426623	55600288	55600408

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 93.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.2416 / max 54.1666, expressed in 1757 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177647	3.4072	1580
177646	2.1982	1335
177645	0.6362	376

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	93.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.08	gold quality
lower esophagus mucosa	UBERON:0035834	91.01	gold quality
mucosa of transverse colon	UBERON:0004991	90.96	gold quality
gastrocnemius	UBERON:0001388	90.41	gold quality
granulocyte	CL:0000094	89.95	gold quality
body of stomach	UBERON:0001161	89.69	gold quality
apex of heart	UBERON:0002098	89.54	gold quality
muscle of leg	UBERON:0001383	89.12	gold quality
skin of abdomen	UBERON:0001416	89.00	gold quality
pancreatic ductal cell	CL:0002079	88.80	silver quality
skin of leg	UBERON:0001511	88.15	gold quality
leukocyte	CL:0000738	86.94	gold quality
monocyte	CL:0000576	86.88	gold quality
minor salivary gland	UBERON:0001830	86.57	gold quality
lower esophagus	UBERON:0013473	86.27	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.25	gold quality
transverse colon	UBERON:0001157	86.05	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.00	gold quality
left coronary artery	UBERON:0001626	85.97	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.87	gold quality
right lobe of liver	UBERON:0001114	85.75	gold quality
popliteal artery	UBERON:0002250	85.66	gold quality
tibial artery	UBERON:0007610	85.64	gold quality
descending thoracic aorta	UBERON:0002345	85.57	gold quality
aorta	UBERON:0000947	85.40	gold quality
thoracic aorta	UBERON:0001515	85.38	gold quality
ascending aorta	UBERON:0001496	85.34	gold quality
esophagus	UBERON:0001043	85.28	gold quality
esophagus mucosa	UBERON:0002469	85.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.91

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2096.1	ZNF524	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

10 targeting ZNF524, 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-4692	100.00	67.32	2066
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-637	97.91	64.05	1517
HSA-MIR-6791-3P	97.45	64.31	1123
HSA-MIR-6836-3P	97.08	64.99	712
HSA-MIR-711	96.60	65.75	528
HSA-MIR-6090	91.01	62.65	222

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp524	ENSMUSG00000051184
rattus_norvegicus	Zfp524	ENSRNOG00000016565

Paralogs (28): ZNF280C (ENSG00000056277), ZBTB25 (ENSG00000089775), PRDM13 (ENSG00000112238), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), NACC2 (ENSG00000148411), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), BCL6B (ENSG00000161940), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF280A (ENSG00000169548), ZNF581 (ENSG00000171425), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

Zinc finger protein 524 — Q96C55 (reviewed: Q96C55)

All UniProt accessions (2): Q96C55, K7EP10

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_694951* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13894, PF13912

UniProt features (25 total): helix 6, strand 5, zinc finger region 4, turn 3, sequence conflict 2, region of interest 2, chain 1, DNA-binding region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7YSF	X-RAY DIFFRACTION	2.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96C55-F1	70.40	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, E2F_Q4, E2F4DP1_01, LFA1_Q6, AAAYRNCTG_UNKNOWN, YY1_Q6, NKX62_Q2, E2F1DP1_01, E2F1DP2_01, YY1_02, CCCNNNNNNAAGWT_UNKNOWN, E2F1_Q3, WHN_B, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, TAATTA_CHX10_01

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

590 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF524	RPS6KL1	Q9Y6S9	711
ZNF524	SNRPN	P14648	531
ZNF524	POLD1	P28340	512
ZNF524	ADK	P55263	418
ZNF524	CXorf38	Q8TB03	397
ZNF524	ZBTB8A	Q96BR9	375
ZNF524	SNAPC2	Q13487	370
ZNF524	MITD1	Q8WV92	370
ZNF524	TMEM102	Q8N9M5	367
ZNF524	ZNF541	Q9H0D2	346
ZNF524	NAIF1	Q69YI7	327
ZNF524	BORCS6	Q96GS4	321
ZNF524	SSC5D	A1L4H1	320
ZNF524	LIPT1	Q9Y234	320
ZNF524	ABRACL	Q9P1F3	313

IntAct

86 interactions, top by confidence:

A	B	Type	Score
SS18L2	GON4L	psi-mi:“MI:0914”(association)	0.610
ZNF524	ZC4H2	psi-mi:“MI:0915”(physical association)	0.560
SERTAD2	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	KRTAP2-4	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	MDFI	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
PICK1	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF526	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	ZNF837	psi-mi:“MI:0915”(physical association)	0.560
TLE5	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
KRTAP1-1	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
GOLGA2	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	ZNF317	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	CARD10	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	ZNF71	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	TSPYL2	psi-mi:“MI:0915”(physical association)	0.560
GRN	ZNF524	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	WFS1	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	KIF1B	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	RNF11	psi-mi:“MI:0915”(physical association)	0.560
ZNF524	SPRED1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (70): ZNF524 (Two-hybrid), YY1AP1 (Affinity Capture-MS), CHD4 (Affinity Capture-MS), C1QBP (Affinity Capture-MS), CHMP1A (Affinity Capture-MS), ADNP (Affinity Capture-MS), THG1L (Affinity Capture-MS), VRK3 (Affinity Capture-MS), ZNF524 (Affinity Capture-MS), ADNP (Affinity Capture-MS), YY1AP1 (Affinity Capture-MS), VRK3 (Affinity Capture-MS), THG1L (Affinity Capture-MS), CHMP1A (Affinity Capture-MS), C1QBP (Affinity Capture-MS)

ESM2 similar proteins: A2CE44, A6NFI3, A6NM28, A8K8V0, O15370, O70218, O95201, P0CJ78, P10075, P10754, P28698, P70338, Q04890, Q07120, Q14V87, Q19A40, Q569E7, Q58DK7, Q5DWN0, Q5FWU5, Q5RJR4, Q5T619, Q5TEC3, Q6DD87, Q6IQX8, Q6PD29, Q6PGE4, Q6ZMY9, Q7Z7K2, Q80VM4, Q8BIF9, Q8JZL0, Q8N8E2, Q8NAF0, Q8NCA9, Q8TD94, Q8WUU4, Q96C55, Q96H86, Q96MX3

Diamond homologs: Q96C55, Q9D0B1, Q9DB38, Q9P0T4, Q9UK33, Q5NBY9, Q9HBE1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	5	13.9×	1e-03

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	45
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

215 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55602074:GCT:G	acceptor_gain	1.0000
19:55600406:G:GT	donor_gain	0.9900
19:55600406:GAGGT:G	donor_loss	0.9900
19:55600408:GGT:G	donor_loss	0.9900
19:55600410:T:A	donor_loss	0.9900
19:55602070:CTTA:C	acceptor_loss	0.9900
19:55602071:TTAG:T	acceptor_loss	0.9900
19:55602072:TA:T	acceptor_loss	0.9900
19:55602073:A:AG	acceptor_gain	0.9900
19:55602073:AGCT:A	acceptor_gain	0.9900
19:55602073:AGCTG:A	acceptor_gain	0.9900
19:55602074:G:A	acceptor_loss	0.9900
19:55602074:G:GA	acceptor_gain	0.9900
19:55602074:GC:G	acceptor_gain	0.9900
19:55602074:GCTG:G	acceptor_gain	0.9900
19:55602074:GCTGG:G	acceptor_gain	0.9900
19:55600406:GAG:G	donor_gain	0.9800
19:55602076:T:A	acceptor_gain	0.9600
19:55600409:G:GG	donor_gain	0.9200
19:55602072:TAG:T	acceptor_gain	0.9200
19:55602071:TTAGC:T	acceptor_gain	0.9100
19:55602074:G:T	acceptor_gain	0.9100
19:55600404:ATGAG:A	donor_gain	0.9000
19:55602073:A:T	acceptor_gain	0.9000
19:55600405:TGAG:T	donor_gain	0.8900
19:55601123:GAC:G	donor_gain	0.8800
19:55600660:GGCGC:G	donor_gain	0.8700
19:55600661:GCGCG:G	donor_gain	0.8700
19:55601138:A:AG	donor_gain	0.8600
19:55602070:CTTAG:C	acceptor_gain	0.8600

AlphaMissense

1675 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55602479:T:C	F123L	1.000
19:55602480:T:C	F123S	1.000
19:55602481:C:A	F123L	1.000
19:55602481:C:G	F123L	1.000
19:55602563:T:C	F151L	1.000
19:55602565:C:A	F151L	1.000
19:55602565:C:G	F151L	1.000
19:55602592:C:A	H160Q	1.000
19:55602592:C:G	H160Q	1.000
19:55602647:T:C	F179L	1.000
19:55602649:C:A	F179L	1.000
19:55602649:C:G	F179L	1.000
19:55602731:T:C	F207L	1.000
19:55602732:T:C	F207S	1.000
19:55602733:T:A	F207L	1.000
19:55602733:T:G	F207L	1.000
19:55602458:T:C	C116R	0.999
19:55602467:T:A	C119S	0.999
19:55602467:T:C	C119R	0.999
19:55602468:G:A	C119Y	0.999
19:55602468:G:C	C119S	0.999
19:55602469:C:G	C119W	0.999
19:55602479:T:A	F123I	0.999
19:55602479:T:G	F123V	0.999
19:55602480:T:G	F123C	0.999
19:55602498:T:C	L129P	0.999
19:55602506:C:A	H132N	0.999
19:55602506:C:G	H132D	0.999
19:55602508:C:A	H132Q	0.999
19:55602508:C:G	H132Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000260260 (19:55597958 C>G), RS1001635941 (19:55598591 T>A,C), RS1001729206 (19:55598347 C>G), RS1001783282 (19:55598025 C>T), RS1002186086 (19:55599797 C>T), RS1002222868 (19:55602597 A>G), RS1003400159 (19:55599367 C>T), RS1003452696 (19:55599257 C>G), RS1003452832 (19:55600433 G>A), RS1003643032 (19:55600287 C>T), RS1004098798 (19:55603265 G>C), RS1004231246 (19:55599672 C>T), RS1005538063 (19:55601984 G>A,C), RS1005845054 (19:55601388 T>G), RS1005926456 (19:55599545 C>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

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	increases expression, affects cotreatment	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arsenic	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Hydrogen Peroxide	affects expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Tobacco Smoke Pollution	increases expression	1
Tunicamycin	increases expression	1
Valproic Acid	decreases expression, increases methylation	1
Aflatoxin B1	decreases methylation	1
Palmitic Acid	increases expression	1
Okadaic Acid	decreases expression	1
Vitamin K 3	affects expression	1
Volatile Organic Compounds	affects 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_XW58	HEK293 eGFP-ZNF524	Transformed cell line	Female

Clinical trials (associated diseases)

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