ZNF202

gene
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Also known as ZKSCAN10ZSCAN42

Summary

ZNF202 (zinc finger protein 202, HGNC:12994) is a protein-coding gene on chromosome 11q23.3, encoding Zinc finger protein 202 (O95125). Transcriptional repressor that binds to elements found predominantly in genes that participate in lipid metabolism.

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in chromosome; nuclear body; and nucleolus.

Source: NCBI Gene 7753 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 69 total
  • MANE Select transcript: NM_003455

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12994
Approved symbolZNF202
Namezinc finger protein 202
Location11q23.3
Locus typegene with protein product
StatusApproved
AliasesZKSCAN10, ZSCAN42
Ensembl geneENSG00000166261
Ensembl biotypeprotein_coding
OMIM603430
Entrez7753

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 34 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000336139, ENST00000525391, ENST00000526252, ENST00000528306, ENST00000529250, ENST00000529691, ENST00000530393, ENST00000530944, ENST00000533463, ENST00000880206, ENST00000880207, ENST00000880208, ENST00000880209, ENST00000880210, ENST00000880211, ENST00000925721, ENST00000925722, ENST00000925723, ENST00000925724, ENST00000925725, ENST00000925726, ENST00000925727, ENST00000925728, ENST00000925729, ENST00000925730, ENST00000925731, ENST00000925732, ENST00000925733, ENST00000925734, ENST00000925735, ENST00000925736, ENST00000925737, ENST00000925738, ENST00000925739, ENST00000965489, ENST00000965490, ENST00000965491

RefSeq mRNA: 4 — MANE Select: NM_003455 NM_001301779, NM_001301780, NM_001301819, NM_003455

CCDS: CCDS8443

Canonical transcript exons

ENST00000530393 — 9 exons

ExonStartEnd
ENSE00001101510123727476123727595
ENSE00001101512123728133123728262
ENSE00001101515123729126123729214
ENSE00001101523123729615123729825
ENSE00001378603123730487123730985
ENSE00001424554123740417123740536
ENSE00001425163123740117123740192
ENSE00002146557123741549123741660
ENSE00003842847123723914123726991

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 87.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3392 / max 75.1101, expressed in 1696 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1229225.33921696

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065587.02gold quality
oocyteCL:000002386.63gold quality
body of pancreasUBERON:000115083.98gold quality
granulocyteCL:000009483.20gold quality
cortical plateUBERON:000534383.03gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.52gold quality
right ovaryUBERON:000211881.92gold quality
ventricular zoneUBERON:000305381.74gold quality
left ovaryUBERON:000211981.63gold quality
left uterine tubeUBERON:000130381.09gold quality
pancreasUBERON:000126481.07gold quality
body of uterusUBERON:000985381.02gold quality
rectumUBERON:000105280.97gold quality
ganglionic eminenceUBERON:000402380.72gold quality
right testisUBERON:000453480.70gold quality
ovaryUBERON:000099280.56gold quality
left testisUBERON:000453380.36gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.93gold quality
monocyteCL:000057679.88gold quality
testisUBERON:000047379.75gold quality
right lobe of thyroid glandUBERON:000111979.62gold quality
gastrocnemiusUBERON:000138879.59gold quality
leukocyteCL:000073879.58gold quality
mononuclear cellCL:000084279.58gold quality
endocervixUBERON:000045879.49gold quality
muscle of legUBERON:000138379.15gold quality
transverse colonUBERON:000115779.14gold quality
spleenUBERON:000210679.05gold quality
stromal cell of endometriumCL:000225578.96gold quality
islet of LangerhansUBERON:000000678.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.56

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

TargetRegulation
ABCA1Repression
ABCG1Repression
AMACRUnknown
APOA1Repression
APOE
FSHRRepression
POMGNT1Repression

Upstream regulators (CollecTRI, top): SCAND1, SOX17

miRNA regulators (miRDB)

70 targeting ZNF202, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-188-3P100.0068.761240
HSA-MIR-450099.9972.722367
HSA-MIR-569699.9872.364487
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-651-3P99.9473.485177
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-368699.9070.532432
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-93-5P99.8873.982606
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-472999.6972.184233
HSA-MIR-366099.6867.331149
HSA-MIR-452699.6867.071136
HSA-MIR-6516-3P99.6568.571238
HSA-MIR-58699.6570.402051
HSA-MIR-570099.6469.882280
HSA-MIR-58799.6470.862611
HSA-MIR-651-5P99.6468.491104

Literature-anchored findings (GeneRIF, showing 4)

  • This is the first study to suggest that ZNF202 could be a new candidate gene for ischemic heart disease and myocardial infarction in the general population. (PMID:16289551)
  • findings show that genetic variation in ZNF202 is common in the general population. However, SNPs in the protein-coding region of ZNF202 do not make a major contribution to HDL cholesterol levels. (PMID:16467280)
  • SOX17-Chromatin immunoprecipitation identified zinc finger protein 202 (Zfp202) as a direct target of SOX17 during endoderm differentiation of F9 embryonal carcinoma cells. (PMID:18523156)
  • Homozygosity for a common functional promoter variant in ZNF202 predicts severe atherosclerosis and an increased risk of IHD. (PMID:18652945)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioplagxENSDARG00000036855
danio_rerioovol1aENSDARG00000076472
danio_rerioplagl2ENSDARG00000076657
danio_rerioovol1bENSDARG00000078256
mus_musculusZfp202ENSMUSG00000025602
rattus_norvegicusZfp202ENSRNOG00000058932
drosophila_melanogasterhbFBGN0001180
drosophila_melanogasterCG12391FBGN0033581
caenorhabditis_elegansWBGENE00001824
caenorhabditis_elegansWBGENE00003033
caenorhabditis_elegansWBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZSCAN18 (ENSG00000121413), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN29 (ENSG00000140265), ZSCAN32 (ENSG00000140987), ZSCAN1 (ENSG00000152467), ZNF18 (ENSG00000154957), ZKSCAN2 (ENSG00000155592), ZNF496 (ENSG00000162714), ZNF641 (ENSG00000167528), ZNF444 (ENSG00000167685), SCAND1 (ENSG00000171222), ZNF274 (ENSG00000171606), ZNF131 (ENSG00000172262), OVOL1 (ENSG00000172818), ZNF518A (ENSG00000177853), ZNF518B (ENSG00000178163), PLAG1 (ENSG00000181690), ZSCAN5B (ENSG00000197213), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300), ZSCAN5C (ENSG00000204532)

Protein

Protein identifiers

Zinc finger protein 202O95125 (reviewed: O95125)

Alternative names: Zinc finger protein with KRAB and SCAN domains 10

All UniProt accessions (4): A0A1D5RMT9, E9PJL4, E9PM99, O95125

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor that binds to elements found predominantly in genes that participate in lipid metabolism. Among its targets are structural components of lipoprotein particles (apolipoproteins AIV, CIII, and E), enzymes involved in lipid processing (lipoprotein lipase, lecithin cholesteryl ester transferase), transporters involved in lipid homeostasis (ABCA1, ABCG1), and several genes involved in processes related to energy metabolism and vascular disease.

Subunit / interactions. Interacts with SDP1.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in testis. Also expressed in breast carcinoma cell lines.

Isoforms (2)

UniProt IDNamesCanonical?
O95125-1Beta, 2yes
O95125-2Alpha, 1

RefSeq proteins (4): NP_001288708, NP_001288709, NP_001288748, NP_003446* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF01352, PF02023

UniProt features (25 total): zinc finger region 8, cross-link 5, sequence conflict 3, domain 2, sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95125-F159.200.05

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 466, 22, 454, 460, 507, 521

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 138 (showing top): BROWNE_HCMV_INFECTION_4HR_UP, MORF_BRCA1, MORF_RAD51L3, MORF_CTSB, BLALOCK_ALZHEIMERS_DISEASE_UP, MORF_IL4, MORF_PRKCA, GOBP_LIPID_METABOLIC_PROCESS, AFP1_Q6, AACTTT_UNKNOWN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MORF_ATF2, MORF_PPP2R5B, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, BROWNE_HCMV_INFECTION_14HR_UP

GO Biological Process (5): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), lipid metabolic process (GO:0006629), regulation of DNA-templated transcription (GO:0006355), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (9): 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), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (4): chromosome (GO:0005694), nucleolus (GO:0005730), nuclear body (GO:0016604), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription3
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
intracellular membraneless organelle3
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
DNA-templated transcription2
negative regulation of DNA-templated transcription1
primary metabolic process1
regulation of gene expression1
regulation of RNA biosynthetic process1
negative regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
transition metal ion binding1
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
DNA binding1
cation binding1
nuclear lumen1
nucleoplasm1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1008 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF202MZF1P28698787
ZNF202ZNF474Q6S9Z5660
ZNF202ADTRPQ96IZ2618
ZNF202ZNF534Q76KX8611
ZNF202SCN3BQ9NY72504
ZNF202STK32BQ9NY57500
ZNF202TBX10O75333495
ZNF202TRMOQ9BU70495
ZNF202STX18Q9P2W9493
ZNF202CRMP1Q14194492
ZNF202EVC2Q86UK5492
ZNF202HEMGNQ9BXL5491
ZNF202WNT11O96014490
ZNF202SATB2Q9UPW6476
ZNF202LCATP04180460

IntAct

77 interactions, top by confidence:

ABTypeScore
KRT40ZNF202psi-mi:“MI:0915”(physical association)0.720
ZNF202KRT40psi-mi:“MI:0915”(physical association)0.720
ZNF202SCAND1psi-mi:“MI:0915”(physical association)0.660
ZNF202SCAND1psi-mi:“MI:0914”(association)0.660
ZNF202LMO4psi-mi:“MI:0915”(physical association)0.600
ZNF202psi-mi:“MI:0915”(physical association)0.560
ZNF202MTIF3psi-mi:“MI:0915”(physical association)0.560
ZNF202CEP70psi-mi:“MI:0915”(physical association)0.560
ZNF202CARD10psi-mi:“MI:0915”(physical association)0.560
ZNF202MCCpsi-mi:“MI:0915”(physical association)0.560
ZNF202ZNF837psi-mi:“MI:0915”(physical association)0.560
ZNF202SSX2IPpsi-mi:“MI:0915”(physical association)0.560
ZNF202MEOX2psi-mi:“MI:0915”(physical association)0.560
ZNF202SEPHS1psi-mi:“MI:0915”(physical association)0.560
ZNF202NAA11psi-mi:“MI:0915”(physical association)0.560
ZNF202MAD2L1BPpsi-mi:“MI:0915”(physical association)0.560
ZNF202NAA10psi-mi:“MI:0915”(physical association)0.560
ZNF202ZNF438psi-mi:“MI:0915”(physical association)0.560
ZNF202ZNF250psi-mi:“MI:0915”(physical association)0.560
ZNF202SCNM1psi-mi:“MI:0915”(physical association)0.560
ZNF202EAF1psi-mi:“MI:0915”(physical association)0.560
ZNF202ZNF835psi-mi:“MI:0915”(physical association)0.560
ZNF202SNX2psi-mi:“MI:0915”(physical association)0.440

BioGRID (35): KRT40 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZNF473 (Two-hybrid), ZMYM2 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), TK1 (Affinity Capture-MS), ZNF202 (Affinity Capture-MS), RCOR3 (Affinity Capture-MS), ZNF202 (Two-hybrid), ZNF202 (Two-hybrid), ZNF202 (Two-hybrid), ZNF202 (Two-hybrid), ZNF202 (Two-hybrid), ZNF202 (Two-hybrid)

ESM2 similar proteins: A1YEQ3, A1YEV9, A1YFW6, A1YG26, A1YG48, A1YG60, A2T6W2, A2T712, A2T736, A2T7L7, A6QNZ0, O14978, O15535, O95125, P17022, P17029, P49910, P51815, P59923, Q07231, Q15776, Q16670, Q1LZ87, Q3MJ62, Q3URR7, Q4KLI1, Q4R8H9, Q53GI3, Q5R670, Q5R741, Q5RJ54, Q63HK3, Q642B9, Q6P9G9, Q810A1, Q86W11, Q8BGS3, Q8CF60, Q8NF99, Q92670

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

1 interactions.

AEffectBMechanism
ZNF202“down-regulates quantity by repression”POMGNT1“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance60
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1490 predictions. Top by Δscore:

VariantEffectΔscore
11:123728126:T:TAdonor_gain1.0000
11:123728128:CTTA:Cdonor_loss1.0000
11:123728131:A:ACdonor_gain1.0000
11:123728131:A:Tdonor_loss1.0000
11:123728132:C:CCdonor_gain1.0000
11:123728132:C:CGdonor_loss1.0000
11:123728132:CA:Cdonor_gain1.0000
11:123728132:CACAG:Cdonor_gain1.0000
11:123728162:T:TAdonor_gain1.0000
11:123729213:CT:Cacceptor_gain1.0000
11:123729215:C:CCacceptor_gain1.0000
11:123729610:C:Adonor_gain1.0000
11:123729620:T:Adonor_gain1.0000
11:123729644:T:TAdonor_gain1.0000
11:123730542:T:TAdonor_gain1.0000
11:123730986:C:CCacceptor_gain1.0000
11:123740432:T:TAdonor_gain1.0000
11:123741547:A:ACdonor_gain1.0000
11:123741548:C:CCdonor_gain1.0000
11:123741548:CGG:Cdonor_gain1.0000
11:123741548:CGGCT:Cdonor_gain1.0000
11:123726989:CTC:Cacceptor_gain0.9900
11:123726993:T:Aacceptor_loss0.9900
11:123727003:G:GCacceptor_gain0.9900
11:123727470:CCTCA:Cdonor_loss0.9900
11:123727471:CTCA:Cdonor_loss0.9900
11:123727472:TCA:Tdonor_loss0.9900
11:123727473:CACC:Cdonor_loss0.9900
11:123727474:ACC:Adonor_loss0.9900
11:123727475:C:Gdonor_loss0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000107100 (11:123731430 C>T), RS1000375346 (11:123725255 A>G), RS1000477735 (11:123731872 A>G), RS1000575230 (11:123741107 G>A), RS1000702029 (11:123731206 C>G,T), RS1000753845 (11:123742025 A>C), RS1000762377 (11:123724115 G>A), RS1000786123 (11:123737326 G>A), RS1001108285 (11:123737013 C>T), RS1001317758 (11:123728962 G>A), RS1001362147 (11:123741507 G>C), RS1001386055 (11:123730820 C>T), RS1001427092 (11:123742968 G>A), RS1001498516 (11:123736306 C>G,T), RS1001569461 (11:123735954 G>C)

Disease associations

OMIM: gene MIM:603430 | 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):

StudyTraitp-value
GCST000514_8Response to antipsychotic therapy (extrapyramidal side effects)4.000000e-07
GCST003802_5Response to citalopram or escitalopram in depression7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression3
Valproic Acidaffects expression, decreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
TAK-243decreases sumoylation1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
ferrous chloridedecreases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Adeninedecreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyrenedecreases methylation1
Cisplatindecreases expression1
Colchicinedecreases expression1
Diurondecreases expression1
Doxorubicindecreases expression1
Estradiolincreases expression1
Ethyl Methanesulfonatedecreases expression1
Etoposidedecreases expression1
Formaldehydedecreases expression1
Herbicidesdecreases expression1
Methyl Methanesulfonatedecreases expression1
Testosteronedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Mitomycindecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_XW17HEK293 eGFP-ZNF202Transformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.