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ZSCAN16

gene
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Also known as FLJ22191dJ265C24.3

Summary

ZSCAN16 (zinc finger and SCAN domain containing 16, HGNC:20813) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger and SCAN domain-containing protein 16 (Q9H4T2). 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 80345 — RefSeq curated summary.

At a glance

  • GWAS associations: 20
  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_025231

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20813
Approved symbolZSCAN16
Namezinc finger and SCAN domain containing 16
Location6p22.1
Locus typegene with protein product
StatusApproved
AliasesFLJ22191, dJ265C24.3
Ensembl geneENSG00000196812
Ensembl biotypeprotein_coding
OMIM618544
Entrez80345

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000340487, ENST00000685330, ENST00000854769, ENST00000854770, ENST00000928538, ENST00000928539, ENST00000928540, ENST00000942452

RefSeq mRNA: 5 — MANE Select: NM_025231 NM_001320555, NM_001320556, NM_001320557, NM_001320558, NM_025231

CCDS: CCDS4644

Canonical transcript exons

ENST00000340487 — 4 exons

ExonStartEnd
ENSE000008485152812678328126921
ENSE000013641472812943028130082
ENSE000014735252812541328125830
ENSE000014735272812460928124677

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 87.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.6382 / max 78.0778, expressed in 1272 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
666124.63821272

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.11gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.26gold quality
ganglionic eminenceUBERON:000402381.74gold quality
mucosa of transverse colonUBERON:000499180.70gold quality
rectumUBERON:000105280.20gold quality
granulocyteCL:000009480.11gold quality
epithelial cell of pancreasCL:000008380.02silver quality
monocyteCL:000057679.61gold quality
leukocyteCL:000073879.43gold quality
mononuclear cellCL:000084279.34gold quality
tendon of biceps brachiiUBERON:000818878.86gold quality
palpebral conjunctivaUBERON:000181278.47gold quality
islet of LangerhansUBERON:000000678.00gold quality
small intestine Peyer’s patchUBERON:000345477.89gold quality
bloodUBERON:000017877.68gold quality
cortical plateUBERON:000534377.64gold quality
transverse colonUBERON:000115777.63gold quality
mucosa of sigmoid colonUBERON:000499377.41gold quality
body of stomachUBERON:000116177.39gold quality
colonic mucosaUBERON:000031777.28gold quality
C1 segment of cervical spinal cordUBERON:000646977.26gold quality
spleenUBERON:000210676.95gold quality
mucosa of stomachUBERON:000119976.80gold quality
minor salivary glandUBERON:000183076.41gold quality
small intestineUBERON:000210876.37gold quality
metanephros cortexUBERON:001053376.14gold quality
epithelium of nasopharynxUBERON:000195175.99silver quality
oocyteCL:000002375.85silver quality
pancreatic ductal cellCL:000207975.71silver quality
intestineUBERON:000016075.66gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.21

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA2100.1ZSCAN16More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:22955616

miRNA regulators (miRDB)

12 targeting ZSCAN16, 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-9-5P100.0072.282361
HSA-MIR-684499.8270.692423
HSA-MIR-391599.4568.491905
HSA-MIR-520A-5P99.3566.721632
HSA-MIR-525-5P99.3566.851615
HSA-MIR-133A-3P99.2771.531270
HSA-MIR-133B99.2771.531270
HSA-MIR-316198.7167.14816
HSA-MIR-3136-5P98.5367.68793
HSA-MIR-443998.5367.53793
HSA-MIR-451198.3267.971500
HSA-MIR-376A-5P97.7065.61863

Literature-anchored findings (GeneRIF, showing 2)

  • ZNF435 proved to be a transcription repressor as its overexpression in AD293 cells inhibited the transcriptional activities of AP-1. (PMID:17646705)
  • ZSCAN16 promotes proliferation, migration and invasion of bladder cancer via regulating NF-kB, AKT, mTOR, P38 and other genes. (PMID:32172065)

Cross-species orthologs

0 orthologs

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), 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), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 16 — Q9H4T2 (reviewed: Q9H4T2)

Alternative names: Zinc finger protein 392, Zinc finger protein 435

All UniProt accessions (1): Q9H4T2

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 (5): NP_001307484, NP_001307485, NP_001307486, NP_001307487, NP_079507* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF02023

UniProt features (19 total): strand 5, zinc finger region 4, helix 3, region of interest 2, chain 1, domain 1, turn 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2COTSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H4T2-F166.970.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): ACEVEDO_LIVER_CANCER_UP, OSMAN_BLADDER_CANCER_DN, CHEN_HOXA5_TARGETS_9HR_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, IL2_UP.V1_DN, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ELF2_TARGET_GENES, NKX2_2_TARGET_GENES, SNAI1_TARGET_GENES, SNIP1_TARGET_GENES, ZNF257_TARGET_GENES, ZNF660_TARGET_GENES, MIR4729

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

GO Molecular Function (7): 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), 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
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

358 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSCAN16NKAPLQ5M9Q1608
ZSCAN16TMEM154Q6P9G4536
ZSCAN16A0A494C0M2A0A494C0M2508
ZSCAN16LRRC63Q05C16447
ZSCAN16RFC1P35251445
ZSCAN16SYTL3Q4VX76427
ZSCAN16ZNF438Q7Z4V0423
ZSCAN16TMEM38AQ9H6F2421
ZSCAN16SMIM7Q9BQ49396
ZSCAN16OR1C1Q15619392
ZSCAN16DLGAP1P78335377
ZSCAN16CT45A3P0DMU6358
ZSCAN16PRR15Q8IV56328
ZSCAN16PRRC2BQ5JSZ5327
ZSCAN16RASAL2Q9UJF2319

IntAct

47 interactions, top by confidence:

ABTypeScore
ZSCAN16ZNF446psi-mi:“MI:0915”(physical association)0.780
ZNF446ZSCAN16psi-mi:“MI:0915”(physical association)0.780
AP1M1ZSCAN16psi-mi:“MI:0915”(physical association)0.560
ZSCAN22ZSCAN16psi-mi:“MI:0915”(physical association)0.560
ZSCAN16psi-mi:“MI:0915”(physical association)0.560
PPLZSCAN16psi-mi:“MI:0915”(physical association)0.560
TRIM41ZSCAN16psi-mi:“MI:0915”(physical association)0.560
ZNF24ZSCAN16psi-mi:“MI:0915”(physical association)0.560
NTAQ1ZSCAN16psi-mi:“MI:0915”(physical association)0.560
SCAND1ZSCAN16psi-mi:“MI:0915”(physical association)0.560
ZSCAN16SPRED1psi-mi:“MI:0915”(physical association)0.560
ZSCAN32ZNF197psi-mi:“MI:0914”(association)0.530
ZNF446ZSCAN16psi-mi:“MI:0915”(physical association)0.370
TRIM63ZSCAN16psi-mi:“MI:0915”(physical association)0.000
TRIM55ZSCAN16psi-mi:“MI:0915”(physical association)0.000
ZNF446ZSCAN16psi-mi:“MI:0915”(physical association)0.000
ZSCAN16psi-mi:“MI:0915”(physical association)0.000
ZSCAN16ZSCAN22psi-mi:“MI:0915”(physical association)0.000

BioGRID (18): ZSCAN16 (Two-hybrid), ZSCAN16 (Affinity Capture-MS), ZSCAN16 (Two-hybrid), ZSCAN16 (Affinity Capture-MS), ZSCAN16 (Two-hybrid), SLC25A38 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (Two-hybrid), ZSCAN16 (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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

600 predictions. Top by Δscore:

VariantEffectΔscore
6:28124677:GGT:Gdonor_loss1.0000
6:28124678:GTG:Gdonor_loss1.0000
6:28126781:A:AGacceptor_gain1.0000
6:28126782:G:GAacceptor_gain1.0000
6:28126782:GGT:Gacceptor_gain1.0000
6:28126782:GGTC:Gacceptor_gain1.0000
6:28126897:G:GTdonor_gain1.0000
6:28126917:GAATG:Gdonor_gain1.0000
6:28126918:A:Tdonor_gain1.0000
6:28126918:AATG:Adonor_gain1.0000
6:28126919:ATG:Adonor_gain1.0000
6:28126919:ATGG:Adonor_loss1.0000
6:28126920:TG:Tdonor_gain1.0000
6:28126921:GG:Gdonor_gain1.0000
6:28126922:G:GGdonor_gain1.0000
6:28126923:T:Gdonor_loss1.0000
6:28124673:GTAAG:Gdonor_gain0.9900
6:28124678:G:GGdonor_gain0.9900
6:28125824:A:Tdonor_gain0.9900
6:28126777:CCCTA:Cacceptor_gain0.9900
6:28126778:CCTA:Cacceptor_gain0.9900
6:28126779:CTA:Cacceptor_gain0.9900
6:28126780:TAGGT:Tacceptor_gain0.9900
6:28126781:AG:Aacceptor_gain0.9900
6:28126781:AGG:Aacceptor_gain0.9900
6:28126782:G:Cacceptor_gain0.9900
6:28126782:GG:Gacceptor_gain0.9900
6:28126782:GGTCC:Gacceptor_gain0.9900
6:28126917:G:GTdonor_gain0.9900
6:28129424:TTACA:Tacceptor_loss0.9900

AlphaMissense

2302 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:28129636:T:CF245L0.998
6:28129638:C:AF245L0.998
6:28129638:C:GF245L0.998
6:28129720:T:CF273L0.998
6:28129722:C:AF273L0.998
6:28129722:C:GF273L0.998
6:28129804:T:CF301L0.998
6:28129806:C:AF301L0.998
6:28129806:C:GF301L0.998
6:28129888:T:CF329L0.998
6:28129890:C:AF329L0.998
6:28129890:C:GF329L0.998
6:28129823:T:CL307P0.997
6:28129833:T:AH310Q0.997
6:28129833:T:GH310Q0.997
6:28129739:T:CL279P0.996
6:28129805:T:CF301S0.996
6:28129831:C:GH310D0.996
6:28129845:C:AH314Q0.996
6:28129845:C:GH314Q0.996
6:28129677:C:AH258Q0.995
6:28129677:C:GH258Q0.995
6:28129835:A:CQ311P0.995
6:28129749:T:AH282Q0.994
6:28129749:T:GH282Q0.994
6:28129831:C:AH310N0.994
6:28129917:T:AH338Q0.994
6:28129917:T:GH338Q0.994
6:28129721:T:CF273S0.993
6:28129915:C:GH338D0.993

dbSNP variants (sampled 300 via entrez): RS1000183590 (6:28128380 CTTACA>C), RS1000361029 (6:28128516 G>C), RS1000818028 (6:28129013 T>C), RS1001594259 (6:28127639 G>A), RS1002198637 (6:28124030 T>C), RS1002587903 (6:28126464 C>T), RS1002944191 (6:28125998 G>A,C), RS1003271212 (6:28125667 A>G), RS1003481040 (6:28125991 A>T), RS1003707056 (6:28125147 C>T), RS1004417208 (6:28129131 T>TA), RS1004551469 (6:28125279 C>G), RS1005021602 (6:28125895 C>T), RS1006144170 (6:28127604 A>T), RS1007211577 (6:28126473 T>C)

Disease associations

OMIM: gene MIM:618544 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

StudyTraitp-value
GCST004521_112Autism spectrum disorder or schizophrenia3.000000e-26
GCST004521_115Autism spectrum disorder or schizophrenia3.000000e-16
GCST004521_163Autism spectrum disorder or schizophrenia3.000000e-08
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
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

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
trichostatin Aaffects cotreatment, decreases expression, affects expression4
Valproic Aciddecreases expression, increases expression2
GSK-J4decreases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
geraniolincreases expression1
mono-(2-ethylhexyl)phthalatedecreases methylation1
ferrous chloridedecreases expression1
avobenzonedecreases expression1
perfluorooctane sulfonic acidincreases expression1
monomethylarsonous acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Vorinostatincreases expression1
Leflunomidedecreases expression1
Air Pollutantsdecreases expression1
Aspirinincreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Estradiolaffects cotreatment, decreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Leadaffects expression1
Methyl Methanesulfonateincreases expression1
Niclosamidedecreases expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HD47HEK293 eGFP-ZSCAN16Transformed 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