ZNF324

Summary

ZNF324 (zinc finger protein 324, HGNC:14096) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 324A (O75467). 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. Acts upstream of or within with a positive effect on G1/S transition of mitotic cell cycle and cell population proliferation. Predicted to be active in nucleus.

Source: NCBI Gene 25799 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 133 total
• MANE Select transcript: NM_014347

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14096
Approved symbol	ZNF324
Name	zinc finger protein 324
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZF5128, ZNF324A
Ensembl gene	ENSG00000083812
Ensembl biotype	protein_coding
OMIM	617477
Entrez	25799

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000196482, ENST00000536459, ENST00000593925, ENST00000868897, ENST00000868898, ENST00000868899, ENST00000868900, ENST00000868901, ENST00000960633, ENST00000960634, ENST00000960635

RefSeq mRNA: 1 — MANE Select: NM_014347 NM_014347

CCDS: CCDS12981

Canonical transcript exons

ENST00000196482 — 4 exons

Exon	Start	End
ENSE00001005524	58467080	58467183
ENSE00002249748	58470731	58475436
ENSE00002437418	58469180	58469306
ENSE00002502706	58469728	58469844

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 81.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4990 / max 118.9985, expressed in 1762 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177847	6.7648	1751
177848	0.7342	444

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	81.21	gold quality
sural nerve	UBERON:0015488	78.35	gold quality
prefrontal cortex	UBERON:0000451	78.31	gold quality
stromal cell of endometrium	CL:0002255	77.81	gold quality
right lobe of liver	UBERON:0001114	77.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.37	gold quality
frontal cortex	UBERON:0001870	77.00	gold quality
granulocyte	CL:0000094	76.67	gold quality
superior frontal gyrus	UBERON:0002661	76.09	gold quality
ventricular zone	UBERON:0003053	75.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.54	gold quality
ganglionic eminence	UBERON:0004023	75.48	gold quality
blood	UBERON:0000178	75.38	gold quality
cerebellum	UBERON:0002037	75.26	gold quality
cerebellar hemisphere	UBERON:0002245	75.22	gold quality
cerebellar cortex	UBERON:0002129	75.18	gold quality
right frontal lobe	UBERON:0002810	75.16	gold quality
adenohypophysis	UBERON:0002196	75.10	gold quality
cerebral cortex	UBERON:0000956	74.74	gold quality
pituitary gland	UBERON:0000007	74.60	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.28	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.21	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	74.09	gold quality
bone marrow	UBERON:0002371	74.08	gold quality
urinary bladder	UBERON:0001255	74.01	gold quality
liver	UBERON:0002107	73.85	gold quality
left uterine tube	UBERON:0001303	73.71	gold quality
mucosa of stomach	UBERON:0001199	73.70	gold quality
esophagus mucosa	UBERON:0002469	73.68	gold quality
skin of leg	UBERON:0001511	73.64	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.84

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1977.1	ZNF324	More than 3 adjacent zinc fingers
MA1977.2	ZNF324	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28273063

miRNA regulators (miRDB)

54 targeting ZNF324, 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-9-5P	100.00	72.28	2361
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-361-5P	98.95	70.16	1340

Literature-anchored findings (GeneRIF, showing 1)

• Biological functions of miRNA-203b-3p/ZNF324 in laryngeal carcinoma. (PMID:38279443)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	42sp43	ENSDARG00000104170
mus_musculus	Zfp324	ENSMUSG00000004500
rattus_norvegicus	Zfp324	ENSRNOG00000027436
drosophila_melanogaster	dwg	FBGN0000520
drosophila_melanogaster	CG6654	FBGN0038301
caenorhabditis_elegans		WBGENE00003933

Paralogs (6): ZBTB47 (ENSG00000114853), GTF3A (ENSG00000122034), ZUP1 (ENSG00000153975), ZNF513 (ENSG00000163795), ZNF652 (ENSG00000198740), ZNF324B (ENSG00000249471)

Protein

Protein identifiers

Zinc finger protein 324A — O75467 (reviewed: O75467)

Alternative names: Zinc finger protein ZF5128

All UniProt accessions (2): O75467, M0R1C8

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation. May be involved in regulation of cell proliferation.

Subcellular location. Nucleus.

Tissue specificity. Expressed at high levels in the spleen, thymus, and PBMC, at low levels in the prostate, ovary, small intestine, colon (mucosal lining), placenta, lung, and pancreas, and very weakly expressed in the liver and kidney.

Induction. Induced at the early stage of T cell activation. Regulated at the transcriptional level during the cell cycle. Induced at a maximum level in the S phase.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (1): NP_055162* (*=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

Pfam: PF00096, PF01352

UniProt features (14 total): zinc finger region 9, region of interest 2, chain 1, domain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75467-F1	64.68	0.39

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway
R-HSA-9843940	Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 71 (showing top): GOBP_CELL_CYCLE_PHASE_TRANSITION, ROVERSI_GLIOMA_COPY_NUMBER_UP, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, MODULE_123, GOBP_MITOTIC_CELL_CYCLE, GOBP_CELL_CYCLE_PROCESS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MARTENS_TRETINOIN_RESPONSE_DN, CSR_EARLY_UP.V1_UP, ATM_DN.V1_UP, RELA_DN.V1_UP, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, PRC2_EZH2_UP.V1_UP, PRC2_SUZ12_UP.V1_UP, PDGF_ERK_DN.V1_DN

GO Biological Process (4): G1/S transition of mitotic cell cycle (GO:0000082), regulation of transcription by RNA polymerase II (GO:0006357), cell population proliferation (GO:0008283), 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-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Regulation of endogenous retroelements	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
mitotic cell cycle	1
mitotic cell cycle phase transition	1
cell cycle G1/S phase transition	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cellular process	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

744 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF324	TRIM28	Q13263	528
ZNF324	ZNF382	Q96SR6	400
ZNF324	ZNF224	P17033	399
ZNF324	GSPT1	P15170	367
ZNF324	GJD3	Q8N144	335
ZNF324	CHERP	Q8IWX8	324
ZNF324	ARHGAP25	P42331	306
ZNF324	UBL3	O95164	298
ZNF324	PHF3	Q92576	295
ZNF324	ERH	P70659	290
ZNF324	RNF26	Q9BY78	271
ZNF324	RAP2C	Q9Y3L5	269
ZNF324	NFRKB	Q6P4R8	256
ZNF324	CLIC3	O95833	249
ZNF324	MGST3	O14880	244

IntAct

58 interactions, top by confidence:

A	B	Type	Score
ZNF169	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF707	ZNF316	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
CACNG5	ZNF316	psi-mi:“MI:0914”(association)	0.530
PRG3	ZNF324	psi-mi:“MI:0914”(association)	0.530
RPF1	ZNF324	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
FBL	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF764	SH3PXD2B	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF324	psi-mi:“MI:0914”(association)	0.530
ZNF460	ZNF324	psi-mi:“MI:0914”(association)	0.530
NOTCH2	ZNF316	psi-mi:“MI:0914”(association)	0.530
Trim28	FTH1	psi-mi:“MI:0915”(physical association)	0.400
ZNF324	RPL4	psi-mi:“MI:0915”(physical association)	0.400
FBL	GXYLT2	psi-mi:“MI:0914”(association)	0.350
NXF2B	MEIOC	psi-mi:“MI:0914”(association)	0.350
RFPL4B	KRBA1	psi-mi:“MI:0914”(association)	0.350
EFEMP1	ZNF316	psi-mi:“MI:0914”(association)	0.350
PSME3	ZNF891	psi-mi:“MI:0914”(association)	0.350
SKAP1	MYO9A	psi-mi:“MI:0914”(association)	0.350

BioGRID (69): ZNF324 (Affinity Capture-RNA), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS), ZNF324 (Affinity Capture-MS)

ESM2 similar proteins: A3KN32, A6NM28, A8K8V0, E9PYI1, O75467, O95201, P10072, P10075, P10078, P10754, P28698, P30373, P52736, Q0VCC5, Q14929, Q16587, Q17QR7, Q29RZ4, Q3KNW1, Q3TDE8, Q3US17, Q58DK7, Q5RJR4, Q5T619, Q5TEC3, Q5U4E2, Q62396, Q68H95, Q6AW86, Q6PGE4, Q6ZMY9, Q7Z398, Q7Z7K2, Q8BI73, Q8BIF9, Q8BIQ3, Q8BKK5, Q8JZL0, Q8N393, Q8R0T2

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	114
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

973 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58467181:A:T	donor_gain	1.0000
19:58469176:TTA:T	acceptor_loss	1.0000
19:58469177:TA:T	acceptor_loss	1.0000
19:58469178:A:AG	acceptor_gain	1.0000
19:58469178:AG:A	acceptor_gain	1.0000
19:58469178:AGGA:A	acceptor_loss	1.0000
19:58469179:G:GT	acceptor_gain	1.0000
19:58469179:GG:G	acceptor_gain	1.0000
19:58469179:GGACC:G	acceptor_gain	1.0000
19:58469302:GCTGG:G	donor_gain	1.0000
19:58469304:TGGG:T	donor_loss	1.0000
19:58469305:GG:G	donor_gain	1.0000
19:58469306:GG:G	donor_gain	1.0000
19:58469306:GGT:G	donor_loss	1.0000
19:58469307:G:C	donor_loss	1.0000
19:58469307:G:GG	donor_gain	1.0000
19:58469308:T:G	donor_loss	1.0000
19:58469723:CACAG:C	acceptor_loss	1.0000
19:58469724:ACAG:A	acceptor_gain	1.0000
19:58469726:A:AG	acceptor_gain	1.0000
19:58469726:A:AT	acceptor_loss	1.0000
19:58469726:AG:A	acceptor_gain	1.0000
19:58469727:G:GA	acceptor_gain	1.0000
19:58469727:GG:G	acceptor_gain	1.0000
19:58469727:GGA:G	acceptor_gain	1.0000
19:58469727:GGAC:G	acceptor_gain	1.0000
19:58469727:GGACT:G	acceptor_gain	1.0000
19:58469831:G:GT	donor_gain	1.0000
19:58469842:CTGG:C	donor_loss	1.0000
19:58469845:G:GG	donor_gain	1.0000

AlphaMissense

3579 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:58471372:T:C	F294L	1.000
19:58471374:C:A	F294L	1.000
19:58471374:C:G	F294L	1.000
19:58471288:T:C	F266L	0.999
19:58471290:C:A	F266L	0.999
19:58471290:C:G	F266L	0.999
19:58471456:T:C	F322L	0.999
19:58471458:C:A	F322L	0.999
19:58471458:C:G	F322L	0.999
19:58471540:T:C	F350L	0.999
19:58471542:C:A	F350L	0.999
19:58471542:C:G	F350L	0.999
19:58471624:T:C	F378L	0.999
19:58471626:C:A	F378L	0.999
19:58471626:C:G	F378L	0.999
19:58471708:T:C	F406L	0.999
19:58471710:C:A	F406L	0.999
19:58471710:C:G	F406L	0.999
19:58471792:T:C	F434L	0.999
19:58471794:T:A	F434L	0.999
19:58471794:T:G	F434L	0.999
19:58471876:T:C	F462L	0.999
19:58471878:C:A	F462L	0.999
19:58471878:C:G	F462L	0.999
19:58471960:T:C	F490L	0.999
19:58471962:C:A	F490L	0.999
19:58471962:C:G	F490L	0.999
19:58471307:T:C	L272P	0.998
19:58471317:C:A	H275Q	0.998
19:58471317:C:G	H275Q	0.998

dbSNP variants (sampled 300 via entrez): RS1000430399 (19:58475937 G>A,C), RS1000441917 (19:58467921 C>T), RS1000787520 (19:58472452 A>G), RS1000955127 (19:58472706 A>T), RS1001156533 (19:58468776 C>T), RS1001498615 (19:58467374 C>A,G,T), RS1001551015 (19:58467533 C>G,T), RS1001678933 (19:58468197 G>A), RS1001897208 (19:58475613 T>C), RS1001950987 (19:58475784 G>A,C), RS1002062748 (19:58471829 T>G), RS1002451723 (19:58472501 G>T), RS1002603678 (19:58473941 C>T), RS1003001846 (19:58470766 G>A,C), RS1003119416 (19:58470595 C>A,T)

Disease associations

OMIM: gene MIM:617477 | 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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
TAK-243	increases sumoylation	1
bisphenol A	affects cotreatment, decreases expression	1
trichostatin A	affects expression	1
ferrous chloride	decreases expression	1
cupric oxide	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Diazinon	increases methylation	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Selenium	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Vitamin E	affects cotreatment, increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Asbestos, Crocidolite	decreases 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_HD20	HEK293 eGFP-ZNF324	Transformed cell line	Female

Clinical trials (associated diseases)

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