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ZSCAN21

gene
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Also known as DKFZp434L134NY-REN-21Zipro1

Summary

ZSCAN21 (zinc finger and SCAN domain containing 21, HGNC:13104) is a protein-coding gene on chromosome 7q22.1, encoding Zinc finger and SCAN domain-containing protein 21 (Q9Y5A6). Strong transcriptional activator.

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 7589 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 39 total
  • MANE Select transcript: NM_145914

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13104
Approved symbolZSCAN21
Namezinc finger and SCAN domain containing 21
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesDKFZp434L134, NY-REN-21, Zipro1
Ensembl geneENSG00000166529
Ensembl biotypeprotein_coding
OMIM601261
Entrez7589

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 16 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000292450, ENST00000438937, ENST00000456748, ENST00000477297, ENST00000906173, ENST00000906174, ENST00000906175, ENST00000906176, ENST00000906177, ENST00000906178, ENST00000906179, ENST00000906180, ENST00000938146, ENST00000938147, ENST00000938148, ENST00000938149, ENST00000938150

RefSeq mRNA: 4 — MANE Select: NM_145914 NM_001362779, NM_001362780, NM_001362781, NM_145914

CCDS: CCDS5681, CCDS87526

Canonical transcript exons

ENST00000292450 — 4 exons

ExonStartEnd
ENSE00001555916100063788100065040
ENSE00001754262100049774100049841
ENSE00003531656100056911100057405
ENSE00003667730100057698100057890

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 96.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.9157 / max 45.5454, expressed in 1696 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
799163.03731548
799171.87841199

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002396.62gold quality
secondary oocyteCL:000065591.91gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.96gold quality
parotid glandUBERON:000183187.96gold quality
cortical plateUBERON:000534386.86gold quality
ventricular zoneUBERON:000305385.91gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.77gold quality
ganglionic eminenceUBERON:000402384.72gold quality
endothelial cellCL:000011584.43silver quality
right uterine tubeUBERON:000130283.55gold quality
gastrocnemiusUBERON:000138883.36gold quality
muscle of legUBERON:000138383.15gold quality
kidney epitheliumUBERON:000481981.99silver quality
hindlimb stylopod muscleUBERON:000425281.92gold quality
tibialis anteriorUBERON:000138581.80silver quality
skeletal muscle organUBERON:001489281.70gold quality
epithelial cell of pancreasCL:000008381.65gold quality
right lobe of liverUBERON:000111481.34gold quality
deltoidUBERON:000147681.13silver quality
muscle layer of sigmoid colonUBERON:003580580.94gold quality
lower esophagus muscularis layerUBERON:003583380.81gold quality
lower esophagusUBERON:001347380.78gold quality
esophagogastric junction muscularis propriaUBERON:003584180.26gold quality
islet of LangerhansUBERON:000000679.98gold quality
smooth muscle tissueUBERON:000113579.97gold quality
adrenal tissueUBERON:001830379.93gold quality
stromal cell of endometriumCL:000225579.86gold quality
calcaneal tendonUBERON:000370179.86gold quality
metanephrosUBERON:000008179.77gold quality
granulocyteCL:000009479.75gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.09

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
SNCAUnknown

JASPAR motifs

MotifNameFamily
MA2336.1ZSCAN21More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:34351703

miRNA regulators (miRDB)

14 targeting ZSCAN21, 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-6875-3P99.8270.262983
HSA-MIR-561-3P99.6470.903647
HSA-MIR-6758-3P99.5767.551078
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-6505-3P99.3467.391071
HSA-MIR-10B-3P99.0466.98988
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-4763-5P98.7563.89854
HSA-MIR-463598.7467.631339
HSA-MIR-446398.5666.051071
HSA-MIR-124-5P98.1167.651095
HSA-MIR-708-3P97.5068.671082
HSA-MIR-5187-3P97.2867.101037
HSA-MIR-476593.1166.17737

Literature-anchored findings (GeneRIF, showing 2)

  • This result indicates that NY-REN-21 can function either as a homodimer or as a heterodimer with SCAND1. (PMID:16540086)
  • deregulation of the TRIM17/TRIM41/ZSCAN21 pathway may be involved in the pathogenesis of Parkinson’s disease. (PMID:30485814)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZscan21ENSMUSG00000037017
rattus_norvegicusZscan21ENSRNOG00000039234

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 21 — Q9Y5A6 (reviewed: Q9Y5A6)

Alternative names: Renal carcinoma antigen NY-REN-21, Zinc finger protein 38 homolog

All UniProt accessions (3): C9JHD9, Q9Y5A6, G3V0F4

UniProt curated annotations — full annotation on UniProt →

Function. Strong transcriptional activator. Plays an important role in spermatogenesis; essential for the progression of meiotic prophase I in spermatocytes.

Subcellular location. Nucleus.

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

RefSeq proteins (4): NP_001349708, NP_001349709, NP_001349710, NP_666019* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF02023, PF13465

UniProt features (17 total): zinc finger region 7, cross-link 4, region of interest 2, compositionally biased region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5A6-F166.330.10

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 (4): 27, 221, 232, 349

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MALE_GAMETE_GENERATION, GOBP_ORGANELLE_FISSION, GOBP_MALE_MEIOSIS_I, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, POU3F2_02, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, HU_GENOTOXIC_DAMAGE_4HR, GOBP_MEIOTIC_CELL_CYCLE, SANSOM_APC_TARGETS, GOBP_CELL_CYCLE_PROCESS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_MALE_MEIOTIC_NUCLEAR_DIVISION, FEVR_CTNNB1_TARGETS_UP

GO Biological Process (8): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), male meiosis I (GO:0007141), spermatogenesis (GO:0007283), cell differentiation (GO:0030154), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of DNA-templated transcription (GO:0045893), meiotic cell cycle (GO:0051321)

GO Molecular Function (8): 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 activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
DNA-templated transcription2
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
male gamete generation2
regulation of transcription by RNA polymerase II2
regulation of gene expression1
regulation of RNA biosynthetic process1
meiosis I1
male meiotic nuclear division1
meiotic cell cycle1
developmental process involved in reproduction1
cellular developmental process1
positive regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
cell cycle1
sexual reproduction1
reproductive process1
meiotic nuclear division1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
double-stranded DNA binding1
sequence-specific DNA binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSCAN21NOX4Q9NPH5768
ZSCAN21TRIM41Q8WV44523
ZSCAN21TVP23AA6NH52430
ZSCAN21TRIM17Q9Y577415
ZSCAN21ZSCAN22P10073396
ZSCAN21SNCAP37840376
ZSCAN21MPGP29372350
ZSCAN21L3MBTL2Q969R5338
ZSCAN21RBM14Q96PK6329
ZSCAN21ZNF219Q9P2Y4320
ZSCAN21OCEL1Q9H607311
ZSCAN21BEND3Q5T5X7287
ZSCAN21FOXP4Q8IVH2287
ZSCAN21A0A0A6YYI9A0A0A6YYI9285
ZSCAN21SLC25A39Q9BZJ4278

IntAct

152 interactions, top by confidence:

ABTypeScore
CDK8MED19psi-mi:“MI:2364”(proximity)0.850
ZSCAN21ZNF24psi-mi:“MI:0915”(physical association)0.830
ZNF24ZSCAN21psi-mi:“MI:0915”(physical association)0.830
ZSCAN21ZNF24psi-mi:“MI:0914”(association)0.830
GRAP2STAMBPpsi-mi:“MI:0914”(association)0.810
GRAP2ZSCAN21psi-mi:“MI:0915”(physical association)0.740
ZKSCAN4ZSCAN21psi-mi:“MI:0915”(physical association)0.740
ZSCAN21ZNF446psi-mi:“MI:0915”(physical association)0.720
KRTAP10-8ZSCAN21psi-mi:“MI:0915”(physical association)0.720
ZNF496ZSCAN21psi-mi:“MI:0915”(physical association)0.720
ZSCAN21KRTAP10-8psi-mi:“MI:0915”(physical association)0.720
ZSCAN21ZNF496psi-mi:“MI:0915”(physical association)0.720
ZNF446ZSCAN21psi-mi:“MI:0915”(physical association)0.720
ZSCAN23ZSCAN21psi-mi:“MI:0915”(physical association)0.670
ZNF213ZSCAN21psi-mi:“MI:0915”(physical association)0.670
KRTAP10-5ZSCAN21psi-mi:“MI:0915”(physical association)0.560
ZSCAN21KRTAP10-9psi-mi:“MI:0915”(physical association)0.560
ZSCAN21KRT40psi-mi:“MI:0915”(physical association)0.560
ZSCAN21TRIM41psi-mi:“MI:0915”(physical association)0.560

BioGRID (137): ZSCAN21 (Two-hybrid), ZNF446 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZNF496 (Two-hybrid), TRIM41 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZSCAN21 (Affinity Capture-MS), ZSCAN21 (Affinity Capture-MS), ZSCAN21 (Affinity Capture-MS), ZSCAN21 (Affinity Capture-MS), ZSCAN21 (Reconstituted Complex)

ESM2 similar proteins: A1YEP8, A1YEV9, A1YFW2, A1YG26, A1YG48, A1YG60, A2T6E3, A2T6V8, A2T712, A2T736, A2T7D2, A2T7F4, A2T7L7, A2T812, A6QNZ0, O14709, O15535, O43296, O43309, P10073, P17023, P17097, P49910, Q07231, Q12901, Q15776, Q16670, Q1LZ87, Q3MJ62, Q53GI3, Q571J5, Q5JNZ3, Q5RAE6, Q5RBX0, Q5RCD9, Q5RJ54, Q7Z7L9, Q86W11, Q8IZ26, Q8NF99

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance31
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

899 predictions. Top by Δscore:

VariantEffectΔscore
7:100057403:CAGG:Cdonor_loss1.0000
7:100057406:GT:Gdonor_loss1.0000
7:100057693:TCTA:Tacceptor_loss1.0000
7:100057694:CTAG:Cacceptor_loss1.0000
7:100057889:AGGTG:Adonor_loss1.0000
7:100057890:GGTGA:Gdonor_loss1.0000
7:100057891:G:GCdonor_loss1.0000
7:100057892:T:Gdonor_loss1.0000
7:100049838:CATGG:Cdonor_loss0.9900
7:100049883:G:GTdonor_gain0.9900
7:100057406:G:GGdonor_gain0.9900
7:100057696:A:AGacceptor_gain0.9900
7:100057697:G:GGacceptor_gain0.9900
7:100052077:A:AGdonor_gain0.9800
7:100057697:GGT:Gacceptor_gain0.9800
7:100057697:GGTC:Gacceptor_gain0.9800
7:100057697:GGTCT:Gacceptor_gain0.9800
7:100058140:AAAG:Aacceptor_gain0.9800
7:100063786:A:AGacceptor_gain0.9800
7:100063787:G:GGacceptor_gain0.9800
7:100063787:GA:Gacceptor_gain0.9800
7:100049842:G:GGdonor_gain0.9700
7:100049879:A:Tdonor_gain0.9700
7:100052077:A:Gdonor_gain0.9700
7:100057696:AG:Aacceptor_gain0.9700
7:100057697:GG:Gacceptor_gain0.9700
7:100057891:G:GGdonor_gain0.9700
7:100063783:TTCAG:Tacceptor_loss0.9700
7:100063785:CA:Cacceptor_loss0.9700
7:100049844:GA:Gdonor_loss0.9600

AlphaMissense

3129 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:100064051:T:CF286L1.000
7:100064053:T:AF286L1.000
7:100064053:T:GF286L1.000
7:100064135:T:CF314L1.000
7:100064137:C:AF314L1.000
7:100064137:C:GF314L1.000
7:100064216:T:CF341L1.000
7:100064218:T:AF341L1.000
7:100064218:T:GF341L1.000
7:100064300:T:CF369L1.000
7:100064302:C:AF369L1.000
7:100064302:C:GF369L1.000
7:100064384:T:CF397L1.000
7:100064386:C:AF397L1.000
7:100064386:C:GF397L1.000
7:100064468:T:CF425L1.000
7:100064470:C:AF425L1.000
7:100064470:C:GF425L1.000
7:100064552:T:CF453L1.000
7:100064554:C:AF453L1.000
7:100064554:C:GF453L1.000
7:100064052:T:CF286S0.999
7:100064070:T:CL292P0.999
7:100064078:C:GH295D0.999
7:100064080:C:AH295Q0.999
7:100064080:C:GH295Q0.999
7:100064092:C:AH299Q0.999
7:100064092:C:GH299Q0.999
7:100064114:T:CC307R0.999
7:100064135:T:AF314I0.999

dbSNP variants (sampled 300 via entrez): RS1000174343 (7:100060508 G>A,C), RS1000547772 (7:100058223 G>A), RS1000637003 (7:100052921 G>A), RS1000798357 (7:100052790 G>A), RS1000911406 (7:100059165 G>C), RS1001301328 (7:100063652 T>C), RS1001500607 (7:100059376 T>C), RS1001587981 (7:100054044 C>T), RS1001640159 (7:100054395 G>A), RS1001802515 (7:100048232 G>A), RS1002358320 (7:100051193 A>T), RS1002410635 (7:100050850 T>C), RS1002593950 (7:100055776 A>T), RS1002594911 (7:100056430 G>A,C), RS1002644932 (7:100056182 G>A,C)

Disease associations

OMIM: gene MIM:601261 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST010002_259Refractive error3.000000e-16
GCST010702_48Subcortical volume (MOSTest)6.000000e-10
GCST010703_289Brain morphology (MOSTest)6.000000e-15

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

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.

ChemicalActions (top 5)PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases expression1
trichostatin Aaffects expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideaffects cotreatment, decreases expression1
Leflunomideincreases expression1
Vehicle Emissionsincreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Indomethacinaffects cotreatment, increases expression1
Manganeseincreases abundance, increases expression1
Methyl Methanesulfonateincreases expression1
Quercetinincreases expression1
Tetrachlorodibenzodioxindecreases expression, affects cotreatment1
Valproic Acidaffects expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Acrylamideincreases expression1
Particulate Matterincreases abundance, increases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_XW92HEK293 eGFP-ZSCAN21Transformed 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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot