ZSCAN9

gene
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Also known as PRD51

Summary

ZSCAN9 (zinc finger and SCAN domain containing 9, HGNC:12984) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger and SCAN domain-containing protein 9 (O15535). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 7746 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 65 total
  • MANE Select transcript: NM_006299

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12984
Approved symbolZSCAN9
Namezinc finger and SCAN domain containing 9
Location6p22.1
Locus typegene with protein product
StatusApproved
AliasesPRD51
Ensembl geneENSG00000137185
Ensembl biotypeprotein_coding
OMIM602246
Entrez7746

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 15 protein_coding, 1 nonsense_mediated_decay

ENST00000252207, ENST00000425468, ENST00000526391, ENST00000527436, ENST00000527844, ENST00000531941, ENST00000531979, ENST00000531981, ENST00000647743, ENST00000866168, ENST00000919061, ENST00000919062, ENST00000950585, ENST00000950586, ENST00000950587, ENST00000950588

RefSeq mRNA: 4 — MANE Select: NM_006299 NM_001199479, NM_001199480, NM_001410841, NM_006299

CCDS: CCDS4646, CCDS56407, CCDS93875

Canonical transcript exons

ENST00000252207 — 4 exons

ExonStartEnd
ENSE000021898162822527528225366
ENSE000036992862822701228227504
ENSE000037017382822769028227837
ENSE000039035062823256228233487

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 89.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.0034 / max 139.8894, expressed in 1751 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
666199.00341751

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402389.51gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.32gold quality
oocyteCL:000002387.19gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.91gold quality
right testisUBERON:000453486.04gold quality
left testisUBERON:000453385.90gold quality
cortical plateUBERON:000534385.73gold quality
cerebellar hemisphereUBERON:000224584.90gold quality
rectumUBERON:000105284.89gold quality
embryoUBERON:000092284.78gold quality
cerebellar cortexUBERON:000212984.66gold quality
testisUBERON:000047384.40gold quality
right hemisphere of cerebellumUBERON:001489084.30gold quality
mucosa of transverse colonUBERON:000499184.23gold quality
ventricular zoneUBERON:000305384.16gold quality
adrenal tissueUBERON:001830384.07gold quality
muscle layer of sigmoid colonUBERON:003580583.92gold quality
body of uterusUBERON:000985383.84gold quality
metanephros cortexUBERON:001053383.70gold quality
lower esophagus muscularis layerUBERON:003583383.66gold quality
lower esophagusUBERON:001347383.65gold quality
adenohypophysisUBERON:000219683.37gold quality
esophagogastric junction muscularis propriaUBERON:003584183.23gold quality
right ovaryUBERON:000211883.12gold quality
apex of heartUBERON:000209883.07gold quality
body of pancreasUBERON:000115082.97gold quality
left ovaryUBERON:000211982.97gold quality
small intestine Peyer’s patchUBERON:000345482.91gold quality
right lobe of thyroid glandUBERON:000111982.90gold quality
transverse colonUBERON:000115782.86gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.64

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
CDKN2A

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

23 targeting ZSCAN9, 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-3613-3P100.0076.367965
HSA-MIR-656-3P100.0072.152788
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5692A100.0074.406850
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-453199.9969.703181
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-875-3P99.6369.472548
HSA-MIR-372-5P99.4169.112299
HSA-MIR-431199.3170.473041
HSA-MIR-4758-3P99.1263.96869
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-315498.9466.551455
HSA-MIR-3124-3P98.8768.952123
HSA-MIR-58398.7167.441791
HSA-MIR-448398.0964.121642
HSA-MIR-191397.0766.201417
HSA-MIR-3126-5P96.8765.83912
HSA-MIR-6875-5P96.8765.49958
HSA-MIR-490-5P96.7565.81661

Cross-species orthologs

0 orthologs

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), 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 9O15535 (reviewed: O15535)

Alternative names: Cell proliferation-inducing gene 12 protein, PRD51, Zinc finger protein 193

All UniProt accessions (6): A0A0B4J224, O15535, E9PLJ4, E9PQL7, U3KQB2, U3KQV4

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 (2)

UniProt IDNamesCanonical?
O15535-11yes
O15535-22

RefSeq proteins (4): NP_001186408, NP_001186409, NP_001397770, NP_006290* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF02023

UniProt features (13 total): zinc finger region 5, cross-link 3, chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15535-F164.000.05

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 (3): 26, 215, 238

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, DANG_BOUND_BY_MYC, SCHLOSSER_SERUM_RESPONSE_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN, PDGF_ERK_DN.V1_DN, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, DIDO1_TARGET_GENES, E2F2_TARGET_GENES, GLI4_TARGET_GENES, GTF2E2_TARGET_GENES, HHEX_TARGET_GENES, HMG20B_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

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), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), 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
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
DNA binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

364 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSCAN9NKAPLQ5M9Q1614
ZSCAN9THUMPD2Q9BTF0336
ZSCAN9FAM180BQ6P0A1323
ZSCAN9MEAK7Q6P9B6321
ZSCAN9HBG1P02096320
ZSCAN9GPR20Q99678311
ZSCAN9TRIM6Q9C030308
ZSCAN9NKAPQ8N5F7305
ZSCAN9TMEM161BQ8NDZ6305
ZSCAN9TM2D1Q9BX74300
ZSCAN9TRIM34Q9BYJ4287
ZSCAN9SMCHD1A6NHR9274
ZSCAN9PGBD1Q96JS3271
ZSCAN9LRRC37AA6NMS7271
ZSCAN9CXorf38Q8TB03269
ZSCAN9STIMATEQ86TL2269

IntAct

105 interactions, top by confidence:

ABTypeScore
ZNF446ZSCAN9psi-mi:“MI:0915”(physical association)0.780
ZSCAN9ZNF446psi-mi:“MI:0915”(physical association)0.780
ZNF446ZSCAN9psi-mi:“MI:0915”(physical association)0.750
ZSCAN9ZNF446psi-mi:“MI:0915”(physical association)0.750
SRPK2ZSCAN9psi-mi:“MI:0915”(physical association)0.720
ZSCAN9SRPK2psi-mi:“MI:0915”(physical association)0.720
ZSCAN9LMO3psi-mi:“MI:0915”(physical association)0.720
LMO3ZSCAN9psi-mi:“MI:0915”(physical association)0.720
ZSCAN9MAGEH1psi-mi:“MI:0915”(physical association)0.560
MAGEH1ZSCAN9psi-mi:“MI:0915”(physical association)0.560
ZSCAN9AIRIMpsi-mi:“MI:0915”(physical association)0.560
ZSCAN9FHL2psi-mi:“MI:0915”(physical association)0.560
ZSCAN9ZSCAN22psi-mi:“MI:0915”(physical association)0.560
ZSCAN9ZSCAN23psi-mi:“MI:0915”(physical association)0.560
ZSCAN9FBXO17psi-mi:“MI:0915”(physical association)0.560
ZSCAN9GEMpsi-mi:“MI:0915”(physical association)0.560
ZSCAN9GFAPpsi-mi:“MI:0915”(physical association)0.560
GRNZSCAN9psi-mi:“MI:0915”(physical association)0.560
ZSCAN9NEFLpsi-mi:“MI:0915”(physical association)0.560
ZSCAN9PPIApsi-mi:“MI:0915”(physical association)0.560
PRKCAZSCAN9psi-mi:“MI:0915”(physical association)0.560

BioGRID (26): ZSCAN9 (Two-hybrid), MAGEH1 (Two-hybrid), ZNF446 (Two-hybrid), ZSCAN9 (Two-hybrid), ZNF24 (Affinity Capture-MS), ZNF446 (Two-hybrid), ZSCAN9 (Two-hybrid), TFF3 (Two-hybrid), ZSCAN9 (Affinity Capture-Western), ZSCAN9 (Two-hybrid), ZSCAN9 (Two-hybrid), ZSCAN9 (Two-hybrid), ZSCAN9 (Two-hybrid), ZSCAN9 (Two-hybrid), GEM (Two-hybrid)

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance61
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

763 predictions. Top by Δscore:

VariantEffectΔscore
6:28225367:G:GGdonor_gain1.0000
6:28227688:AGAT:Aacceptor_gain1.0000
6:28227689:GATG:Gacceptor_gain1.0000
6:28225362:GTCTC:Gdonor_gain0.9900
6:28227117:G:Aacceptor_gain0.9900
6:28227687:CAGAT:Cacceptor_loss0.9900
6:28227688:A:AGacceptor_gain0.9900
6:28227688:A:ATacceptor_loss0.9900
6:28227689:G:GAacceptor_loss0.9900
6:28227689:G:GGacceptor_gain0.9900
6:28227689:GAT:Gacceptor_gain0.9900
6:28228161:G:GTdonor_gain0.9900
6:28232560:A:AGacceptor_gain0.9900
6:28232561:G:GGacceptor_gain0.9900
6:28227116:T:TAacceptor_gain0.9800
6:28227500:ATGAG:Adonor_loss0.9800
6:28227501:TGAGG:Tdonor_loss0.9800
6:28227503:AGG:Adonor_loss0.9800
6:28227505:G:Cdonor_loss0.9800
6:28227506:T:Gdonor_loss0.9800
6:28227688:AGATG:Aacceptor_gain0.9800
6:28227689:GATGG:Gacceptor_gain0.9800
6:28227834:ACAG:Adonor_loss0.9800
6:28227835:CAG:Cdonor_loss0.9800
6:28227836:AGGT:Adonor_loss0.9800
6:28227837:GG:Gdonor_loss0.9800
6:28227838:GTGAG:Gdonor_loss0.9800
6:28227839:T:Adonor_loss0.9800
6:28227833:GACAG:Gdonor_gain0.9700
6:28232556:TTTCA:Tacceptor_loss0.9700

AlphaMissense

2611 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:28232864:T:CF291L0.998
6:28232866:C:AF291L0.998
6:28232866:C:GF291L0.998
6:28233116:T:CF375L0.998
6:28233118:T:AF375L0.998
6:28233118:T:GF375L0.998
6:28232948:T:CF319L0.997
6:28232950:C:AF319L0.997
6:28232950:C:GF319L0.997
6:28232780:T:CF263L0.996
6:28232782:T:AF263L0.996
6:28232782:T:GF263L0.996
6:28233063:A:CQ357P0.995
6:28232967:T:CL325P0.994
6:28232977:T:AH328Q0.994
6:28232977:T:GH328Q0.994
6:28233061:T:AH356Q0.994
6:28233061:T:GH356Q0.994
6:28233135:T:CL381P0.994
6:28232893:C:AH300Q0.993
6:28232893:C:GH300Q0.993
6:28233123:G:CR377P0.993
6:28232949:T:CF319S0.992
6:28233051:T:CL353P0.992
6:28232865:T:CF291S0.991
6:28232891:C:GH300D0.991
6:28232975:C:GH328D0.991
6:28233039:G:CR349P0.991
6:28233073:C:AH360Q0.991
6:28233073:C:GH360Q0.991

dbSNP variants (sampled 300 via entrez): RS1000335920 (6:28232972 C>T), RS1000483708 (6:28226537 A>G), RS1000572502 (6:28226889 C>A,T), RS1001230493 (6:28228365 G>A), RS1001317540 (6:28223199 C>G), RS1001565029 (6:28233575 G>C), RS1002449375 (6:28230003 A>C,G), RS1002467234 (6:28231308 A>G), RS1002580500 (6:28230099 C>T), RS1002750158 (6:28231019 C>T), RS1003007135 (6:28225063 G>A,T), RS1004366295 (6:28228481 C>T), RS1004418705 (6:28228705 A>T), RS1004475826 (6:28230727 A>C), RS1004569345 (6:28231010 A>G)

Disease associations

OMIM: gene MIM:602246 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

StudyTraitp-value
GCST004521_112Autism spectrum disorder or schizophrenia3.000000e-26
GCST004521_115Autism spectrum disorder or schizophrenia3.000000e-16
GCST004521_166Autism spectrum disorder or schizophrenia4.000000e-24
GCST004521_212Autism spectrum disorder or schizophrenia5.000000e-14
GCST004521_22Autism spectrum disorder or schizophrenia2.000000e-11
GCST004521_23Autism spectrum disorder or schizophrenia2.000000e-11
GCST004521_6Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_73Autism spectrum disorder or schizophrenia8.000000e-11
GCST004521_77Autism spectrum disorder or schizophrenia1.000000e-19
GCST006088_38Familial squamous cell lung carcinoma5.000000e-07
GCST008921_6Asthma and major depressive disorder1.000000e-09
GCST010002_50Refractive error4.000000e-34
GCST010142_16Fish- and plant-related diet2.000000e-10
GCST010142_19Fish- and plant-related diet4.000000e-10
GCST010142_34Fish- and plant-related diet7.000000e-09
GCST010142_35Fish- and plant-related diet8.000000e-09
GCST010142_42Fish- and plant-related diet1.000000e-08
GCST010142_7Fish- and plant-related diet3.000000e-12
GCST010702_75Subcortical volume (MOSTest)3.000000e-11
GCST010703_272Brain morphology (MOSTest)7.000000e-16
GCST011494_26Daytime nap3.000000e-18
GCST012228_156Waist-hip index4.000000e-08
GCST012230_279Waist-to-hip ratio adjusted for BMI2.000000e-08
GCST90011898_139Alanine aminotransferase levels3.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0006953family history of lung cancer
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement
EFO:0007828daytime rest measurement
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, decreases methylation7
bisphenol Aaffects cotreatment, increases expression2
aristolochic acid Idecreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
bisphenol Faffects cotreatment, increases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
trichostatin Adecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
potassium chromate(VI)increases expression, affects cotreatment1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, increases expression1
di-n-butylphosphoric acidaffects expression1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
dorsomorphindecreases expression, affects cotreatment1
bisphenol Saffects cotreatment, increases expression1
Temozolomideincreases expression1
Catechinaffects cotreatment, decreases expression1
Dexamethasoneincreases expression, affects cotreatment1
Ethyl Methanesulfonateincreases expression1
Indomethacinaffects cotreatment, increases expression1
Methyl Methanesulfonateincreases expression1
Thiramincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cyclosporineincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_AW48K562 eGFP-ZSCAN9Cancer cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): squamous cell lung carcinoma