ZNF492

Summary

ZNF492 (zinc finger protein 492, HGNC:23707) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 492 (Q9P255). May be involved in transcriptional regulation. It is a common-essential gene (DepMap: required in 95.5% of cancer cell lines).

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 57615 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 111 total
• Cancer dependency (DepMap): dependent in 95.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_020855

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23707
Approved symbol	ZNF492
Name	zinc finger protein 492
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1473
Ensembl gene	ENSG00000229676
Ensembl biotype	protein_coding
OMIM	620124
Entrez	57615

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000456783

RefSeq mRNA: 1 — MANE Select: NM_020855 NM_020855

CCDS: CCDS46032

Canonical transcript exons

ENST00000456783 — 4 exons

Exon	Start	End
ENSE00001754325	22663800	22667671
ENSE00002284207	22634324	22634474
ENSE00002303732	22653307	22653433
ENSE00002314461	22653920	22654015

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 81.84.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8725 / max 66.3633, expressed in 535 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174904	1.8087	529
174905	0.0638	29

Top tissues by expression

201 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	81.84	gold quality
buccal mucosa cell	CL:0002336	80.91	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.68	gold quality
ventricular zone	UBERON:0003053	73.16	gold quality
ganglionic eminence	UBERON:0004023	70.79	gold quality
embryo	UBERON:0000922	62.59	gold quality
cortical plate	UBERON:0005343	59.37	silver quality
oviduct epithelium	UBERON:0004804	56.58	silver quality
lower lobe of lung	UBERON:0008949	54.84	silver quality
islet of Langerhans	UBERON:0000006	54.52	gold quality
upper leg skin	UBERON:0004262	54.11	gold quality
bone marrow cell	CL:0002092	53.96	gold quality
endothelial cell	CL:0000115	52.48	gold quality
epithelial cell of pancreas	CL:0000083	52.15	silver quality
pancreatic ductal cell	CL:0002079	52.12	silver quality
bone marrow	UBERON:0002371	51.92	gold quality
smooth muscle tissue	UBERON:0001135	51.58	gold quality
endometrium	UBERON:0001295	51.49	gold quality
cranial nerve II	UBERON:0000941	51.14	silver quality
rectum	UBERON:0001052	51.11	gold quality
fallopian tube	UBERON:0003889	50.33	gold quality
lymph node	UBERON:0000029	49.95	gold quality
adrenal tissue	UBERON:0018303	49.79	silver quality
calcaneal tendon	UBERON:0003701	49.78	silver quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
hair follicle	UBERON:0002073	49.18	gold quality
quadriceps femoris	UBERON:0001377	49.12	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.53

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
RPE65

miRNA regulators (miRDB)

133 targeting ZNF492, 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-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• This KRAB-zinc finger protein serves as a moderate transcriptional factor for Rpe65 gene upregulation. (PMID:16714237)
• Data revealed that hypermethylation of ZNF492 and GPR149 was significantly associated with shorter timetoprogression of patients with clear cell renal cell carcinoma (ccRCC). Hypermethylation of ZNF492 and GPR149 may be independent predictors of tumor progression. Similarly, the methylation status of these two genes was significantly associated with poor outcomes in the independent external validation cohort. (PMID:31115548)

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 492 — Q9P255 (reviewed: Q9P255)

Alternative names: Zinc finger protein 115

All UniProt accessions (1): Q9P255

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_065906* (*=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096

UniProt features (16 total): zinc finger region 13, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P255-F1	72.66	0.27

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 60 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, chr19p12, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HSD17B8_TARGET_GENES, PRKDC_TARGET_GENES, MIR548N, MIR559, MIR548Y

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

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), 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	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF492	ANKRD20A2P	Q5SQ80	477
ZNF492	ANKRD20A4P	Q4UJ75	476
ZNF492	KRTAP19-2	Q3LHN2	447
ZNF492	SATL1	Q86VE3	432
ZNF492	OR13A1	Q8NGR1	419
ZNF492	KRABD4	Q5JUW0	418
ZNF492	Q6GMV1	Q6GMV1	417
ZNF492	FAM72B	Q86X60	410
ZNF492	TCEANC	Q8N8B7	405
ZNF492	GPR149	Q86SP6	400
ZNF492	C12orf42	Q96LP6	396
ZNF492	TMEM121B	Q9BXQ6	390
ZNF492	FAM72D	Q6L9T8	382
ZNF492	FAM72C	H0Y354	381
ZNF492	ZNG1C	Q5JTY5	370
ZNF492	FAM72A	Q5TYM5	370

IntAct

9 interactions, top by confidence:

A	B	Type	Score
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF492	NOMO1	psi-mi:“MI:0915”(physical association)	0.400
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF726	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF492	HPR	psi-mi:“MI:0914”(association)	0.350
ZNF675	LDHC	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): ZNF492 (Proximity Label-MS), ZNF492 (Affinity Capture-MS), ZNF492 (Affinity Capture-MS), PPM1H (Affinity Capture-MS), ZNF492 (Affinity Capture-MS), ZNF492 (Affinity Capture-MS), HPR (Affinity Capture-MS), SPATA33 (Affinity Capture-MS), ZNF492 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), ZNF492 (Affinity Capture-MS), ZNF492 (Negative Genetic)

ESM2 similar proteins: A6NK75, A6NNF4, A6NP11, A8MTY0, A8MUV8, B4DXR9, C9JN71, O75346, O75373, O95780, P0CJ79, P0DKX0, P0DPD5, P17019, P17035, P35789, Q03923, Q03938, Q08AN1, Q14593, Q15928, Q3SXZ3, Q3ZCX4, Q5MCW4, Q5R9S5, Q5RER9, Q68DY1, Q6JLC9, Q6ZMV8, Q6ZN06, Q6ZN08, Q6ZNA1, Q76KX8, Q86T29, Q86V71, Q8IYN0, Q8N4W9, Q8N7M2, Q8NEM1, Q8TD23

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	96
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

567 predictions. Top by Δscore:

Variant	Effect	Δscore
19:22651446:GTTC:G	donor_gain	1.0000
19:22653306:GGGA:G	acceptor_gain	1.0000
19:22653394:A:T	donor_gain	1.0000
19:22653917:CAGGT:C	acceptor_loss	1.0000
19:22653918:AGGT:A	acceptor_loss	1.0000
19:22634440:C:G	donor_gain	0.9900
19:22634474:GGTG:G	donor_loss	0.9900
19:22634476:T:A	donor_loss	0.9900
19:22651450:A:AG	donor_gain	0.9900
19:22651451:G:GG	donor_gain	0.9900
19:22653301:TTTCA:T	acceptor_loss	0.9900
19:22653302:TTCA:T	acceptor_loss	0.9900
19:22653303:TCAGG:T	acceptor_loss	0.9900
19:22653304:CA:C	acceptor_loss	0.9900
19:22653304:CAGGG:C	acceptor_gain	0.9900
19:22653305:A:AG	acceptor_gain	0.9900
19:22653305:AG:A	acceptor_gain	0.9900
19:22653305:AGG:A	acceptor_gain	0.9900
19:22653305:AGGGA:A	acceptor_gain	0.9900
19:22653306:G:GC	acceptor_loss	0.9900
19:22653306:G:GG	acceptor_gain	0.9900
19:22653306:GG:G	acceptor_gain	0.9900
19:22653306:GGG:G	acceptor_gain	0.9900
19:22653306:GGGAG:G	acceptor_gain	0.9900
19:22653429:CGTGG:C	donor_loss	0.9900
19:22653430:GTGG:G	donor_gain	0.9900
19:22653431:TGGG:T	donor_loss	0.9900
19:22653432:GG:G	donor_gain	0.9900
19:22653433:GG:G	donor_gain	0.9900
19:22653434:G:GG	donor_gain	0.9900

AlphaMissense

3536 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:22664453:T:C	F262L	0.990
19:22664455:T:A	F262L	0.990
19:22664455:T:G	F262L	0.990
19:22664873:T:C	F402L	0.985
19:22664875:T:A	F402L	0.985
19:22664875:T:G	F402L	0.985
19:22664537:T:C	F290L	0.982
19:22664539:T:A	F290L	0.982
19:22664539:T:G	F290L	0.982
19:22664285:T:C	F206L	0.981
19:22664287:T:A	F206L	0.981
19:22664287:T:G	F206L	0.981
19:22664369:T:C	F234L	0.981
19:22664371:T:A	F234L	0.981
19:22664371:T:G	F234L	0.981
19:22664957:T:C	F430L	0.979
19:22664959:T:A	F430L	0.979
19:22664959:T:G	F430L	0.979
19:22664621:T:C	F318L	0.975
19:22664623:T:A	F318L	0.975
19:22664623:T:G	F318L	0.975
19:22664292:G:C	R208P	0.965
19:22664892:T:C	L408P	0.961
19:22664705:T:C	F346L	0.950
19:22664707:T:A	F346L	0.950
19:22664707:T:G	F346L	0.950
19:22664789:T:C	F374L	0.950
19:22664791:T:A	F374L	0.950
19:22664791:T:G	F374L	0.950
19:22664388:T:C	L240P	0.949

dbSNP variants (sampled 300 via entrez): RS1000079659 (19:22651573 C>G), RS1000233324 (19:22663617 CTTTAA>C), RS1000661517 (19:22667502 C>T), RS1000796770 (19:22667621 A>G), RS1000915325 (19:22634776 A>T), RS1001037510 (19:22646484 T>G), RS1001163740 (19:22654599 C>T), RS1001373881 (19:22645012 C>T), RS1001496566 (19:22638905 C>A,T), RS1001656705 (19:22644711 T>C), RS1001842296 (19:22649283 T>A), RS1001855594 (19:22634213 G>A), RS1002043098 (19:22655540 A>G), RS1002107895 (19:22657294 C>G,T), RS1002244006 (19:22661420 A>T)

Disease associations

OMIM: gene MIM:620124 | 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
GCST002415_3	Colorectal cancer (diet interaction)	4.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Copper	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases methylation, increases abundance	1
Folic Acid	decreases expression	1
Gold	decreases expression	1
Methotrexate	increases expression	1
Selenium	decreases expression	1
Silicon Dioxide	increases expression	1
Vanadates	decreases expression	1
Vitamin E	decreases expression	1

Clinical trials (associated diseases)

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