ZNF493

Summary

ZNF493 (zinc finger protein 493, HGNC:23708) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 493 (Q6ZR52). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 284443 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 131 total
• MANE Select transcript: NM_001076678

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23708
Approved symbol	ZNF493
Name	zinc finger protein 493
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36504
Ensembl gene	ENSG00000196268
Ensembl biotype	protein_coding
Entrez	284443

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000339914, ENST00000355504, ENST00000392288, ENST00000594390, ENST00000596302, ENST00000596815, ENST00000598152, ENST00000599461, ENST00000599517

RefSeq mRNA: 3 — MANE Select: NM_001076678 NM_001076678, NM_145326, NM_175910

CCDS: CCDS12411, CCDS12412, CCDS42536

Canonical transcript exons

ENST00000392288 — 4 exons

Exon	Start	End
ENSE00001657638	21405761	21405856
ENSE00001822205	21422913	21427577
ENSE00003465138	21405129	21405255
ENSE00003577272	21397133	21397267

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 92.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.5962 / max 191.9413, expressed in 1481 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174888	8.1842	1470
174889	0.4120	242

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
visceral pleura	UBERON:0002401	92.85	gold quality
trabecular bone tissue	UBERON:0002483	91.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.73	gold quality
corpus callosum	UBERON:0002336	91.35	gold quality
cerebellar cortex	UBERON:0002129	91.26	gold quality
cerebellar hemisphere	UBERON:0002245	91.26	gold quality
buccal mucosa cell	CL:0002336	91.16	gold quality
cerebellum	UBERON:0002037	90.34	gold quality
nipple	UBERON:0002030	90.15	gold quality
tibia	UBERON:0000979	90.09	gold quality
calcaneal tendon	UBERON:0003701	89.38	gold quality
colonic epithelium	UBERON:0000397	89.28	gold quality
parietal pleura	UBERON:0002400	89.06	gold quality
adrenal tissue	UBERON:0018303	88.90	gold quality
pleura	UBERON:0000977	88.82	gold quality
cerebellar vermis	UBERON:0004720	88.78	gold quality
cortical plate	UBERON:0005343	88.77	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.60	gold quality
inferior vagus X ganglion	UBERON:0005363	88.47	gold quality
lateral globus pallidus	UBERON:0002476	88.34	gold quality
renal medulla	UBERON:0000362	88.24	gold quality
corpus epididymis	UBERON:0004359	88.14	gold quality
adult organism	UBERON:0007023	88.11	gold quality
germinal epithelium of ovary	UBERON:0001304	88.09	gold quality
mammalian vulva	UBERON:0000997	88.00	gold quality
biceps brachii	UBERON:0001507	87.88	gold quality
substantia nigra pars reticulata	UBERON:0001966	87.85	gold quality
cardia of stomach	UBERON:0001162	87.76	gold quality
caput epididymis	UBERON:0004358	87.75	gold quality
left ovary	UBERON:0002119	87.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.73

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2555.1	ZNF493	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

119 targeting ZNF493, 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-3925-3P	100.00	69.95	1237
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358

Cross-species orthologs

0 orthologs

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 493 — Q6ZR52 (reviewed: Q6ZR52)

All UniProt accessions (4): Q6ZR52, M0QXT4, M0QY95, M0R1U0

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6ZR52-1	1	yes
Q6ZR52-2	2
Q6ZR52-3	3

RefSeq proteins (3): NP_001070146, NP_663299, NP_787106 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (34 total): zinc finger region 22, sequence conflict 6, splice variant 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZR52-F1	78.37	0.09

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 118 (showing top): chr19p12, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, OSMAN_BLADDER_CANCER_DN, NUYTTEN_EZH2_TARGETS_DN, THUM_SYSTOLIC_HEART_FAILURE_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, LU_EZH2_TARGETS_DN, 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_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), 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
transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
regulation of 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
negative regulation of transcription by RNA polymerase II	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF493	psi-mi:“MI:0915”(physical association)	0.370
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): ZNF493 (Synthetic Lethality), ZNF493 (Two-hybrid), ZNF493 (Two-hybrid), ZNF493 (Affinity Capture-MS), ZNF493 (Affinity Capture-MS), ZNF493 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2VDQ7, A6NK75, A6NN14, A6NNF4, A8MQ14, A8MTY0, A8MXY4, B7Z6K7, E9QAG8, O43345, O75290, O75373, O75437, P0CJ79, P10751, P17017, P17019, P17035, P17038, P18749, P35789, P51522, Q03923, Q03938, Q05481, Q14585, Q3SYV7, Q4V348, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6P5C7, Q6ZN08, Q6ZN57, Q6ZR52, Q86V71, Q86XN6, Q8IYB9, Q8N7Q3

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q15928, Q3KNS6, Q3MIS6, Q3SXZ3, Q4R6C2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1323 predictions. Top by Δscore:

Variant	Effect	Δscore
19:21405216:A:T	donor_gain	1.0000
19:21397233:C:G	donor_gain	0.9900
19:21397420:GCC:G	donor_gain	0.9900
19:21405125:TCAG:T	acceptor_loss	0.9900
19:21405126:CA:C	acceptor_loss	0.9900
19:21405127:AGG:A	acceptor_gain	0.9900
19:21405128:GGG:G	acceptor_gain	0.9900
19:21405251:CTTGG:C	donor_loss	0.9900
19:21405254:GG:G	donor_gain	0.9900
19:21405254:GGGTG:G	donor_loss	0.9900
19:21405255:GG:G	donor_gain	0.9900
19:21405255:GGTGA:G	donor_loss	0.9900
19:21405256:GTGAG:G	donor_loss	0.9900
19:21405257:T:A	donor_loss	0.9900
19:21422911:A:AG	acceptor_gain	0.9900
19:21422912:G:GG	acceptor_gain	0.9900
19:21398473:AT:A	donor_gain	0.9800
19:21405127:A:AG	acceptor_gain	0.9800
19:21405127:AG:A	acceptor_gain	0.9800
19:21405128:G:GG	acceptor_gain	0.9800
19:21405128:GG:G	acceptor_gain	0.9800
19:21405256:G:GG	donor_gain	0.9800
19:21405258:G:GT	donor_loss	0.9800
19:21411188:G:GC	acceptor_gain	0.9800
19:21422912:GTT:G	acceptor_gain	0.9800
19:21397323:TGGG:T	donor_gain	0.9700
19:21397326:G:T	donor_gain	0.9700
19:21398148:G:GG	donor_gain	0.9700
19:21405127:AGGG:A	acceptor_gain	0.9700
19:21405128:GGGG:G	acceptor_gain	0.9700

AlphaMissense

5164 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:21424319:T:C	F426L	0.987
19:21424321:T:A	F426L	0.987
19:21424321:T:G	F426L	0.987
19:21424487:T:C	F482L	0.984
19:21424489:T:A	F482L	0.984
19:21424489:T:G	F482L	0.984
19:21424151:T:C	F370L	0.983
19:21424153:T:A	F370L	0.983
19:21424153:T:G	F370L	0.983
19:21424235:T:C	F398L	0.983
19:21424237:T:A	F398L	0.983
19:21424237:T:G	F398L	0.983
19:21424571:T:C	F510L	0.981
19:21424573:T:A	F510L	0.981
19:21424573:T:G	F510L	0.981
19:21424655:T:C	F538L	0.981
19:21424657:T:A	F538L	0.981
19:21424657:T:G	F538L	0.981
19:21424326:G:C	R428P	0.980
19:21424403:T:C	F454L	0.978
19:21424405:T:A	F454L	0.978
19:21424405:T:G	F454L	0.978
19:21424823:T:C	F594L	0.977
19:21424825:T:A	F594L	0.977
19:21424825:T:G	F594L	0.977
19:21424907:T:C	F622L	0.977
19:21424909:T:A	F622L	0.977
19:21424909:T:G	F622L	0.977
19:21423815:T:C	F258L	0.975
19:21423817:T:A	F258L	0.975

dbSNP variants (sampled 300 via entrez): RS1000125386 (19:21398980 G>C), RS1000171469 (19:21416736 C>A,T), RS1000182307 (19:21418585 A>G), RS1000223196 (19:21412729 C>T), RS1000333157 (19:21407096 C>T), RS1000667046 (19:21417008 A>G), RS1000762241 (19:21418143 C>T), RS1000850720 (19:21407307 G>A,T), RS1000871376 (19:21404193 T>C), RS1000875908 (19:21399819 A>G), RS1000944521 (19:21404586 A>T), RS1000996560 (19:21414847 A>AT), RS1001048992 (19:21415042 C>T), RS1001239016 (19:21417665 G>T), RS1001541883 (19:21408004 T>C,G)

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

2 associations (top):

Study	Trait	p-value
GCST002928_10	Nickel levels	1.000000e-07
GCST008163_575	Height	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
mercuric bromide	decreases expression, affects cotreatment	2
Formaldehyde	increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects cotreatment, increases expression, decreases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, decreases expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression	1
aflatoxin B2	decreases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Clorgyline	increases expression	1
Coal	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Smoke	decreases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	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_XW52	HEK293 eGFP-ZNF493	Transformed cell line	Female

Clinical trials (associated diseases)

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