ZNF724

Summary

ZNF724 (zinc finger protein 724, HGNC:32460) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 724 (A8MTY0). 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 DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 440519 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• MANE Select transcript: NM_001355404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32460
Approved symbol	ZNF724
Name	zinc finger protein 724
Location	19p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196081
Ensembl biotype	protein_coding
Entrez	440519

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000418100, ENST00000597037, ENST00000597537

RefSeq mRNA: 2 — MANE Select: NM_001355404 NM_001355404, NM_001355405

CCDS: CCDS86737

Canonical transcript exons

ENST00000418100 — 4 exons

Exon	Start	End
ENSE00001599470	23221599	23224018
ENSE00001630447	23250240	23250394
ENSE00002227214	23231266	23231361
ENSE00003671019	23232167	23232293

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 84.58.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7707 / max 383.8826, expressed in 1248 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180261	7.7707	1248

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.93	gold quality
ganglionic eminence	UBERON:0004023	74.81	gold quality
ventricular zone	UBERON:0003053	74.38	gold quality
adrenal tissue	UBERON:0018303	68.52	gold quality
bone marrow	UBERON:0002371	67.41	gold quality
stromal cell of endometrium	CL:0002255	66.96	gold quality
cortical plate	UBERON:0005343	66.14	gold quality
bone marrow cell	CL:0002092	65.46	silver quality
endometrium	UBERON:0001295	63.02	gold quality
calcaneal tendon	UBERON:0003701	62.67	gold quality
islet of Langerhans	UBERON:0000006	62.50	gold quality
tonsil	UBERON:0002372	62.26	gold quality
lymph node	UBERON:0000029	59.54	gold quality
placenta	UBERON:0001987	57.60	gold quality
corpus callosum	UBERON:0002336	57.57	gold quality
rectum	UBERON:0001052	57.30	gold quality
leukocyte	CL:0000738	56.33	gold quality
monocyte	CL:0000576	55.79	gold quality
vermiform appendix	UBERON:0001154	55.35	gold quality
smooth muscle tissue	UBERON:0001135	55.04	gold quality
gall bladder	UBERON:0002110	53.58	gold quality
lower esophagus mucosa	UBERON:0035834	52.61	gold quality
urinary bladder	UBERON:0001255	51.00	gold quality
superior frontal gyrus	UBERON:0002661	49.97	gold quality
muscle tissue	UBERON:0002385	49.70	gold quality
esophagus mucosa	UBERON:0002469	49.61	gold quality
cortex of kidney	UBERON:0001225	49.45	gold quality
prefrontal cortex	UBERON:0000451	49.15	gold quality
pancreas	UBERON:0001264	49.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.82

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2690.1	ZNF724	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

Literature-anchored findings (GeneRIF, showing 1)

• The present study revealed three gout specific loci, CNTN5, MIR302F, ZNF724, to be clearly associated with mechanisms of gout development, which distinctly differ from the known gout risk loci that basically elevate serum uric acid level. This meta-analysis is the first to reveal the loci associated with crystal-induced inflammation, the last step in gout development that aggravates asymptomatic hyperuricaemia into gout. (PMID:31289104)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp738	ENSMUSG00000048280
mus_musculus	Zfp457	ENSMUSG00000055341
mus_musculus	Zfp595	ENSMUSG00000057842
mus_musculus	Zfp953	ENSMUSG00000098905
rattus_norvegicus	AABR07009105.1	ENSRNOG00000053325

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 724 — A8MTY0 (reviewed: A8MTY0)

All UniProt accessions (3): A8MTY0, M0R0Z7, M0R3J2

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 (2): NP_001342333, NP_001342334 (=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 (19 total): zinc finger region 16, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MTY0-F1	75.50	0.25

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 25 (showing top): chr19p12, FISCHER_DREAM_TARGETS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ZWANG_DOWN_BY_2ND_EGF_PULSE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, HSD17B8_TARGET_GENES, PRKDC_TARGET_GENES, SETD7_TARGET_GENES, ZNF22_TARGET_GENES, ZNF329_TARGET_GENES, ZNF711_TARGET_GENES

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), 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
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	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
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

160 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF724	DHX8	Q14562	484
ZNF724	CNIH2	Q6PI25	394
ZNF724	SHLD2	Q86V20	377
ZNF724	NIPAL1	Q6NVV3	371
ZNF724	CNIH4	Q9P003	365
ZNF724	ASRGL1	Q7L266	364
ZNF724	PAIP1	Q9H074	349
ZNF724	SLC17A1	Q14916	311
ZNF724	CELF4	Q9BZC1	310
ZNF724	CNTN5	O94779	288
ZNF724	NDUFB9	Q9Y6M9	271
ZNF724	CHML	P26374	271
ZNF724	CUX2	O14529	268
ZNF724	DHRS4L2	Q6PKH6	264
ZNF724	CHM	P24386	250

IntAct

49 interactions, top by confidence:

A	B	Type	Score
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
ZNF512	ZNF724	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TIMM50	ZNF724	psi-mi:“MI:0914”(association)	0.530
ZNF724	DHRS2	psi-mi:“MI:0915”(physical association)	0.400
LMNA	ZNF724	psi-mi:“MI:0914”(association)	0.350
APP	ZNF724	psi-mi:“MI:0914”(association)	0.350
CDX1	ZNF724	psi-mi:“MI:0914”(association)	0.350
TIMM50	ZNF724	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
CBX5	ZNF568	psi-mi:“MI:0914”(association)	0.350
ZNF724	CENPB	psi-mi:“MI:0914”(association)	0.350
PRKACA	ZNF724	psi-mi:“MI:0914”(association)	0.350
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL7L1	ZNF320	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF467	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZKSCAN8	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOP2	ZNF320	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 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
Regulation of expression of SLITs and ROBOs	5	13.8×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

736 predictions. Top by Δscore:

Variant	Effect	Δscore
19:23224014:CATAC:C	acceptor_gain	1.0000
19:23224016:TAC:T	acceptor_gain	1.0000
19:23224016:TACC:T	acceptor_loss	1.0000
19:23224017:ACC:A	acceptor_loss	1.0000
19:23224019:CTGAA:C	acceptor_loss	1.0000
19:23231265:C:CA	donor_loss	1.0000
19:23231359:TAC:T	acceptor_gain	1.0000
19:23231360:ACCTG:A	acceptor_loss	1.0000
19:23231363:T:C	acceptor_loss	1.0000
19:23231367:T:TC	acceptor_gain	1.0000
19:23231370:T:TC	acceptor_gain	1.0000
19:23232161:TCTCA:T	donor_loss	1.0000
19:23232162:CTCAC:C	donor_loss	1.0000
19:23232163:TCA:T	donor_loss	1.0000
19:23232164:CACC:C	donor_loss	1.0000
19:23232165:A:AC	donor_gain	1.0000
19:23232165:AC:A	donor_gain	1.0000
19:23232166:C:CC	donor_gain	1.0000
19:23232166:CC:C	donor_gain	1.0000
19:23232206:T:A	donor_gain	1.0000
19:23232291:TCC:T	acceptor_gain	1.0000
19:23232292:CC:C	acceptor_gain	1.0000
19:23232292:CCC:C	acceptor_gain	1.0000
19:23232293:CC:C	acceptor_gain	1.0000
19:23232293:CCTGA:C	acceptor_loss	1.0000
19:23232294:C:CC	acceptor_gain	1.0000
19:23232295:T:G	acceptor_loss	1.0000
19:23224015:ATAC:A	acceptor_gain	0.9900
19:23224017:AC:A	acceptor_gain	0.9900
19:23224018:CC:C	acceptor_gain	0.9900

AlphaMissense

4122 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:23223036:A:C	F403L	0.992
19:23223036:A:T	F403L	0.992
19:23223038:A:G	F403L	0.992
19:23223204:A:C	F347L	0.992
19:23223204:A:T	F347L	0.992
19:23223206:A:G	F347L	0.992
19:23222952:A:C	F431L	0.990
19:23222952:A:T	F431L	0.990
19:23222954:A:G	F431L	0.990
19:23222700:A:C	F515L	0.989
19:23222700:A:T	F515L	0.989
19:23222702:A:G	F515L	0.989
19:23222784:A:C	F487L	0.989
19:23222784:A:T	F487L	0.989
19:23222786:A:G	F487L	0.989
19:23223019:A:G	L409P	0.983
19:23223120:A:C	F375L	0.982
19:23223120:A:T	F375L	0.982
19:23223122:A:G	F375L	0.982
19:23222532:A:C	F571L	0.981
19:23222532:A:T	F571L	0.981
19:23222534:A:G	F571L	0.981
19:23223288:A:C	F319L	0.979
19:23223288:A:T	F319L	0.979
19:23223290:A:G	F319L	0.979
19:23222448:A:C	F599L	0.978
19:23222448:A:T	F599L	0.978
19:23222450:A:G	F599L	0.978
19:23222868:A:C	F459L	0.978
19:23222868:A:T	F459L	0.978

dbSNP variants (sampled 300 via entrez): RS1000021845 (19:23248940 C>T), RS1000074040 (19:23248738 T>A), RS1000393064 (19:23238036 A>G), RS1000424179 (19:23236717 A>C), RS1000633417 (19:23244118 G>A), RS1000673735 (19:23242187 C>A,T), RS1000729649 (19:23236597 TA>T,TAA), RS1000760996 (19:23237886 A>T), RS1000770957 (19:23229620 T>G), RS1000890895 (19:23247653 T>C), RS1000964744 (19:23242077 A>G), RS1001005106 (19:23248061 A>G), RS1001199304 (19:23229624 A>C), RS1001227485 (19:23246476 G>A,C,T), RS1001341983 (19:23246704 G>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

1 associations (top):

Study	Trait	p-value
GCST008460_8	Gout vs. Hyperuricemia	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009104	hyperuricemia

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Oxygen	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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