ZSCAN18

gene
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Also known as FLJ12895

Summary

ZSCAN18 (zinc finger and SCAN domain containing 18, HGNC:21037) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 18 (Q8TBC5). 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 transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 65982 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 98 total
  • MANE Select transcript: NM_001145543

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21037
Approved symbolZSCAN18
Namezinc finger and SCAN domain containing 18
Location19q13.43
Locus typegene with protein product
StatusApproved
AliasesFLJ12895
Ensembl geneENSG00000121413
Ensembl biotypeprotein_coding
Entrez65982

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 33 protein_coding, 5 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000240727, ENST00000421612, ENST00000433686, ENST00000594191, ENST00000594567, ENST00000595721, ENST00000595784, ENST00000595944, ENST00000596372, ENST00000598497, ENST00000600318, ENST00000600404, ENST00000600522, ENST00000600845, ENST00000600897, ENST00000601063, ENST00000601144, ENST00000861637, ENST00000861638, ENST00000861639, ENST00000861640, ENST00000861641, ENST00000861642, ENST00000861643, ENST00000861644, ENST00000861645, ENST00000861646, ENST00000861647, ENST00000861648, ENST00000861649, ENST00000861650, ENST00000861651, ENST00000861652, ENST00000861653, ENST00000932259, ENST00000932260, ENST00000932261, ENST00000941784, ENST00000941785

RefSeq mRNA: 4 — MANE Select: NM_001145543 NM_001145542, NM_001145543, NM_001145544, NM_023926

CCDS: CCDS12971, CCDS46214, CCDS46215

Canonical transcript exons

ENST00000601144 — 7 exons

ExonStartEnd
ENSE000008225075808731658087404
ENSE000030049825809817458098231
ENSE000031275395808385658085379
ENSE000035927055808690658087008
ENSE000036021445808986558090386
ENSE000036795155808617458086266
ENSE000037889305808868858088837

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8075 / max 146.6726, expressed in 1557 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18293214.42571556
1829330.2770100
1829310.104742

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130298.44gold quality
pituitary glandUBERON:000000797.66gold quality
adenohypophysisUBERON:000219697.65gold quality
nucleus accumbensUBERON:000188297.16gold quality
postcentral gyrusUBERON:000258197.13gold quality
hypothalamusUBERON:000189897.10gold quality
right frontal lobeUBERON:000281097.05gold quality
right lobe of thyroid glandUBERON:000111997.03gold quality
left lobe of thyroid glandUBERON:000112096.94gold quality
thyroid glandUBERON:000204696.73gold quality
caudate nucleusUBERON:000187396.71gold quality
right hemisphere of cerebellumUBERON:001489096.71gold quality
Brodmann (1909) area 9UBERON:001354096.67gold quality
cerebellar hemisphereUBERON:000224596.65gold quality
cingulate cortexUBERON:000302796.64gold quality
anterior cingulate cortexUBERON:000983596.64gold quality
cerebellar cortexUBERON:000212996.62gold quality
parietal lobeUBERON:000187296.54gold quality
left ovaryUBERON:000211996.41gold quality
putamenUBERON:000187496.37gold quality
cerebellumUBERON:000203796.33gold quality
amygdalaUBERON:000187696.32gold quality
cardiac muscle of right atriumUBERON:000337996.26gold quality
forebrainUBERON:000189096.23gold quality
Ammon’s hornUBERON:000195496.22gold quality
lower esophagus muscularis layerUBERON:003583396.22gold quality
dorsolateral prefrontal cortexUBERON:000983496.21gold quality
superior frontal gyrusUBERON:000266196.20gold quality
lower esophagusUBERON:001347396.19gold quality
temporal lobeUBERON:000187196.15gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.24

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
CDKN2A

miRNA regulators (miRDB)

21 targeting ZSCAN18, 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-4455100.0065.481587
HSA-MIR-130599.9171.433443
HSA-MIR-467999.7669.191229
HSA-MIR-132499.4666.571302
HSA-MIR-3922-3P99.2564.961136
HSA-MIR-317699.2564.35954
HSA-MIR-4774-3P98.9067.82737
HSA-MIR-797798.6566.182590
HSA-MIR-1178-3P98.5767.09890
HSA-MIR-550A-3P98.3769.61632
HSA-MIR-126298.1766.52757
HSA-MIR-4701-3P98.1766.25788
HSA-MIR-6736-5P98.1766.43760
HSA-MIR-200C-5P97.7167.73596
HSA-MIR-3127-5P97.5265.24786
HSA-MIR-3121-5P97.3066.621146
HSA-MIR-3152-5P96.9866.88819
HSA-MIR-4474-5P94.2367.95568
HSA-MIR-509093.2860.8694
HSA-MIR-6775-5P92.4361.00132
HSA-MIR-609091.0162.65222

Literature-anchored findings (GeneRIF, showing 3)

  • A high negative correlation between promoter DNA methylation and gene expression was observed for CDO1, ZNF331 and ZSCAN18 in gastrointestinal tumors. (PMID:24948044)
  • Inactivation of ZSCAN18 by promoter hypermethylation drives the proliferation via attenuating TP53INP2-mediated autophagy in gastric cancer cells. (PMID:36650573)
  • Zinc finger and SCAN domain-containing protein 18 is a potential DNA methylation-modified tumor suppressor and biomarker in breast cancer. (PMID:37223020)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioplagxENSDARG00000036855
danio_rerioovol1aENSDARG00000076472
danio_rerioplagl2ENSDARG00000076657
danio_rerioovol1bENSDARG00000078256
mus_musculusZscan18ENSMUSG00000070822
rattus_norvegicusZscan18ENSRNOG00000026861
drosophila_melanogasterhbFBGN0001180
drosophila_melanogasterCG12391FBGN0033581
caenorhabditis_elegansWBGENE00001824
caenorhabditis_elegansWBGENE00003033
caenorhabditis_elegansWBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN29 (ENSG00000140265), ZSCAN32 (ENSG00000140987), ZSCAN1 (ENSG00000152467), ZNF18 (ENSG00000154957), ZKSCAN2 (ENSG00000155592), ZNF496 (ENSG00000162714), ZNF202 (ENSG00000166261), 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 and SCAN domain-containing protein 18Q8TBC5 (reviewed: Q8TBC5)

Alternative names: Zinc finger protein 447

All UniProt accessions (8): A0A0C4DG78, Q8TBC5, M0QXJ0, M0QZ65, M0R111, M0R1U9, M0R364, M0R3C6

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.

Isoforms (4)

UniProt IDNamesCanonical?
Q8TBC5-11yes
Q8TBC5-22
Q8TBC5-33
Q8TBC5-44

RefSeq proteins (4): NP_001139014, NP_001139015, NP_001139016, NP_076415 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily
IPR050916SCAN-C2H2_zinc_fingerFamily

Pfam: PF02023

UniProt features (19 total): compositionally biased region 5, region of interest 5, splice variant 3, zinc finger region 2, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TBC5-F153.990.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, ROSS_LEUKEMIA_WITH_MLL_FUSIONS, GATA1_01, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, ACEVEDO_LIVER_CANCER_UP, TGCCTTA_MIR124A, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, HUTTMANN_B_CLL_POOR_SURVIVAL_UP, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, LIM_MAMMARY_LUMINAL_MATURE_UP, ONKEN_UVEAL_MELANOMA_DN, EGFR_UP.V1_DN, WINTER_HYPOXIA_DN

GO Biological Process (1): 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), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

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 binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

670 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSCAN18CDO1P78513678
ZSCAN18DCLK1O15075613
ZSCAN18SFRP1Q8N474570
ZSCAN18KLHL35Q6PF15507
ZSCAN18ZNF331Q9NQX6423
ZSCAN18ATP5MC2Q06055403
ZSCAN18CNRIP1Q96F85399
ZSCAN18CORO6Q6QEF8392
ZSCAN18CCDC8Q9H0W5391
ZSCAN18FOXI2Q6ZQN5391
ZSCAN18ANKUB1A6NFN9369
ZSCAN18SCUBE3Q8IX30367
ZSCAN18RUBCNLQ9H714348
ZSCAN18SCAND1P57086342
ZSCAN18WDR17Q8IZU2336

IntAct

67 interactions, top by confidence:

ABTypeScore
MSH2MSH3psi-mi:“MI:0914”(association)0.920
CSNK1A1FAM83Gpsi-mi:“MI:0914”(association)0.900
PGBD1ZNF24psi-mi:“MI:0914”(association)0.900
ZSCAN18PGBD1psi-mi:“MI:0915”(physical association)0.740
SCAND1ZSCAN18psi-mi:“MI:0915”(physical association)0.740
ZSCAN18SCAND1psi-mi:“MI:0914”(association)0.740
EPM2AIP1ZSCAN18psi-mi:“MI:0915”(physical association)0.670
ZSCAN18SUFUpsi-mi:“MI:0915”(physical association)0.670
ZNF397ZNF213psi-mi:“MI:0914”(association)0.640
ZSCAN18FDXACB1psi-mi:“MI:0915”(physical association)0.560
ZSCAN22ZSCAN18psi-mi:“MI:0915”(physical association)0.560
ZNF174ZSCAN18psi-mi:“MI:0915”(physical association)0.560
ZSCAN18ZNF446psi-mi:“MI:0915”(physical association)0.560
ZSCAN32ZNF197psi-mi:“MI:0914”(association)0.530
PGBD1ZNF213psi-mi:“MI:0914”(association)0.530
ZNF396ZNF24psi-mi:“MI:0914”(association)0.530
ZNF213ZNF24psi-mi:“MI:0914”(association)0.530
ZSCAN18ZNF24psi-mi:“MI:0914”(association)0.530
ZNF215SCAND1psi-mi:“MI:0914”(association)0.530
ZKSCAN4FN1psi-mi:“MI:0914”(association)0.530
ZSCAN9SCAND1psi-mi:“MI:0914”(association)0.530
HOXD4ZSCAN18psi-mi:“MI:0915”(physical association)0.370
LIG4ZSCAN18psi-mi:“MI:0915”(physical association)0.370
SAFB2ZSCAN18psi-mi:“MI:0915”(physical association)0.370
MAPTMEX3Apsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
GLI2SPOPpsi-mi:“MI:0914”(association)0.350
FGFR2LANCL1psi-mi:“MI:0914”(association)0.350
ZKSCAN8ZNF320psi-mi:“MI:0914”(association)0.350

BioGRID (68): ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), ZSCAN18 (Two-hybrid), ZSCAN18 (Two-hybrid), ZSCAN18 (Two-hybrid), PGBD1 (Two-hybrid), SCAND1 (Two-hybrid)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PR82, A1YGK1, A2T7E6, A4D1S0, A6NEL2, A6QP24, A6QPM6, O43593, O43918, O94850, O95873, P0C7X2, P50617, P97609, Q3B7M4, Q3UM83, Q5FWE3, Q5JPB2, Q5M844, Q5XJV6, Q61645, Q64322, Q6GQX2, Q6NZ36, Q6PE13, Q6UWD8, Q6ZMS7, Q6ZW13, Q76NI1, Q7Z6P3, Q8BWG4, Q8BZW2, Q8IWN7, Q8NBB4, Q8NDX1, Q8NHY3, Q8TBC5, Q8TER5, Q91XA5

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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:

PathwayPartnersFoldFDR
Hedgehog ‘on’ state524.0×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance84
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1360 predictions. Top by Δscore:

VariantEffectΔscore
19:58086168:CCTCA:Cdonor_loss1.0000
19:58086169:CTCA:Cdonor_loss1.0000
19:58086170:TCA:Tdonor_loss1.0000
19:58086171:CAC:Cdonor_loss1.0000
19:58086187:T:TAdonor_gain1.0000
19:58086262:ATACC:Aacceptor_gain1.0000
19:58086263:TACC:Tacceptor_gain1.0000
19:58086264:ACC:Aacceptor_gain1.0000
19:58086264:ACCC:Aacceptor_loss1.0000
19:58086265:CC:Cacceptor_gain1.0000
19:58086265:CCC:Cacceptor_gain1.0000
19:58086266:CC:Cacceptor_gain1.0000
19:58086267:C:CCacceptor_gain1.0000
19:58086267:C:Tacceptor_gain1.0000
19:58086271:G:Cacceptor_gain1.0000
19:58086271:G:GCacceptor_gain1.0000
19:58086276:G:Cacceptor_gain1.0000
19:58086276:G:GCacceptor_gain1.0000
19:58086277:T:Cacceptor_gain1.0000
19:58086277:T:TCacceptor_gain1.0000
19:58086285:C:CTacceptor_gain1.0000
19:58086905:CCCCA:Cdonor_gain1.0000
19:58086921:T:TAdonor_gain1.0000
19:58087311:CCCA:Cdonor_loss1.0000
19:58087313:CAC:Cdonor_loss1.0000
19:58087315:C:CAdonor_loss1.0000
19:58087400:CCAGG:Cacceptor_gain1.0000
19:58087401:CAGG:Cacceptor_gain1.0000
19:58087401:CAGGC:Cacceptor_gain1.0000
19:58087402:AGG:Aacceptor_gain1.0000

AlphaMissense

3282 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:58084952:G:CF422L0.999
19:58084952:G:TF422L0.999
19:58084954:A:GF422L0.999
19:58084868:G:CF450L0.998
19:58084868:G:TF450L0.998
19:58084870:A:GF450L0.998
19:58084935:A:GL428P0.997
19:58089977:G:CF97L0.995
19:58089977:G:TF97L0.995
19:58089979:A:GF97L0.995
19:58090059:A:GL70P0.995
19:58090101:A:TV56D0.995
19:58084841:G:CH459Q0.994
19:58084841:G:TH459Q0.994
19:58084891:A:GC443R0.994
19:58084953:A:GF422S0.994
19:58084975:A:GC415R0.994
19:58089987:A:GL94P0.994
19:58089996:A:GL91P0.994
19:58090113:A:GF52S0.994
19:58084869:A:GF450S0.993
19:58084880:G:CC446W0.993
19:58084882:A:GC446R0.993
19:58089978:A:GF97S0.993
19:58084881:C:TC446Y0.992
19:58084925:G:CH431Q0.992
19:58084925:G:TH431Q0.992
19:58084964:G:CC418W0.992
19:58084965:C:GC418S0.992
19:58084966:A:TC418S0.992

dbSNP variants (sampled 300 via entrez): RS1000049058 (19:58105744 T>C), RS1000158585 (19:58088238 A>G), RS1000202331 (19:58112861 G>C), RS1000313220 (19:58091212 A>G), RS1000324608 (19:58118028 G>C), RS1000357595 (19:58116583 C>G,T), RS1000378340 (19:58118233 C>A), RS1000399095 (19:58105522 G>A), RS1000811893 (19:58116852 T>C,G), RS1000824719 (19:58085504 C>A,G,T), RS1000841590 (19:58112607 C>T), RS1000893946 (19:58112758 T>C), RS1000900323 (19:58098195 C>A,G), RS1000949850 (19:58113990 C>T), RS1000955570 (19:58098308 A>G,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects cotreatment, decreases expression5
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, decreases expression, affects cotreatment2
aristolochic acid Iincreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
pirinixic acidincreases expression, affects binding, increases activity1
bisphenol Aaffects cotreatment, decreases methylation1
geraniolincreases expression1
arsenitedecreases expression, increases methylation1
sodium arsenitedecreases expression1
potassium chromate(VI)increases expression1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment1
pentabromodiphenyl etherincreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
LDN 193189affects cotreatment, increases expression1
NSC 689534increases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Benzo(a)pyrenedecreases methylation, increases methylation1
Fluorouracilaffects response to substance1
Mitoxantroneaffects response to substance1
Ozoneincreases oxidation, increases abundance, affects cotreatment1
Polychlorinated Biphenylsaffects expression1
Smokedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_XW90HEK293 eGFP-ZSCAN18Transformed 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.