ZSCAN23

Summary

ZSCAN23 (zinc finger and SCAN domain containing 23, HGNC:21193) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger and SCAN domain-containing protein 23 (Q3MJ62). 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 222696 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_001012455

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21193
Approved symbol	ZSCAN23
Name	zinc finger and SCAN domain containing 23
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	dJ29K1.3.1
Ensembl gene	ENSG00000187987
Ensembl biotype	protein_coding
Entrez	222696

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000289788, ENST00000481983, ENST00000486481, ENST00000855448, ENST00000855449, ENST00000855450, ENST00000926088, ENST00000926089

RefSeq mRNA: 1 — MANE Select: NM_001012455 NM_001012455

CCDS: CCDS47393

Canonical transcript exons

ENST00000289788 — 4 exons

Exon	Start	End
ENSE00001873388	28443399	28443491
ENSE00001889168	28432655	28435078
ENSE00002190752	28435859	28436343
ENSE00003553852	28435460	28435607

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 81.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.8995 / max 178.9283, expressed in 1071 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72419	3.6234	1047
72418	0.2761	131

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	81.94	gold quality
ganglionic eminence	UBERON:0004023	80.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.41	gold quality
cortical plate	UBERON:0005343	79.34	gold quality
adrenal tissue	UBERON:0018303	74.25	gold quality
stromal cell of endometrium	CL:0002255	72.16	gold quality
smooth muscle tissue	UBERON:0001135	70.57	gold quality
islet of Langerhans	UBERON:0000006	70.25	gold quality
calcaneal tendon	UBERON:0003701	70.15	gold quality
left ovary	UBERON:0002119	68.03	gold quality
right ovary	UBERON:0002118	66.57	gold quality
body of uterus	UBERON:0009853	65.23	gold quality
right lobe of thyroid gland	UBERON:0001119	65.17	gold quality
endocervix	UBERON:0000458	64.48	gold quality
left lobe of thyroid gland	UBERON:0001120	64.29	gold quality
cerebellar cortex	UBERON:0002129	64.27	gold quality
cerebellar hemisphere	UBERON:0002245	64.22	gold quality
right hemisphere of cerebellum	UBERON:0014890	64.12	gold quality
ovary	UBERON:0000992	63.92	gold quality
descending thoracic aorta	UBERON:0002345	63.78	gold quality
thyroid gland	UBERON:0002046	63.77	gold quality
gall bladder	UBERON:0002110	63.75	gold quality
rectum	UBERON:0001052	63.62	gold quality
pancreas	UBERON:0001264	63.53	gold quality
corpus callosum	UBERON:0002336	62.77	gold quality
cerebellum	UBERON:0002037	62.68	gold quality
popliteal artery	UBERON:0002250	62.59	gold quality
tibial artery	UBERON:0007610	62.54	gold quality
prefrontal cortex	UBERON:0000451	62.38	gold quality
right coronary artery	UBERON:0001625	62.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting ZSCAN23, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-218-5P	99.93	72.22	2103

Literature-anchored findings (GeneRIF, showing 1)

• Epigenetic silencing ZSCAN23 promotes pancreatic cancer growth by activating Wnt signaling. (PMID:38226836)

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), 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 23 — Q3MJ62 (reviewed: Q3MJ62)

Alternative names: Zinc finger protein 390, Zinc finger protein 453

All UniProt accessions (2): Q3MJ62, G3V1D5

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 (1): NP_001012458* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily

Pfam: PF00096, PF02023

UniProt features (7 total): zinc finger region 5, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3MJ62-F1	65.25	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, SNIP1_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF30_TARGET_GENES, ZNF664_TARGET_GENES, MIR335_3P, MIR4262, MIR494_3P, MIR1200, MIR6756_5P, MIR6766_5P, MIR4703_5P, MIR3185, MIR3942_5P

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:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

334 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN23	VARS2	Q5ST30	566
ZSCAN23	TRIM40	Q6P9F5	535
ZSCAN23	CDSN	Q15517	495
ZSCAN23	TRIM10	Q9UDY6	457
ZSCAN23	R3HDM2	Q9Y2K5	431
ZSCAN23	SMIM10L2A	P0DMW4	419
ZSCAN23	CWH43	Q9H720	394
ZSCAN23	SMIM21	Q3B7S5	391
ZSCAN23	C6orf47	O95873	390
ZSCAN23	PTPN22	Q9Y2R2	387
ZSCAN23	DCAF4L1	Q3SXM0	370
ZSCAN23	C5orf24	Q7Z6I8	370
ZSCAN23	SYTL3	Q4VX76	366
ZSCAN23	UBALD1	Q8TB05	358
ZSCAN23	BLTP3B	A0JNW5	348

IntAct

84 interactions, top by confidence:

A	B	Type	Score
SCAND1	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN23	ZSCAN21	psi-mi:“MI:0915”(physical association)	0.670
ZNF24	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN23	LHPP	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	ZNF446	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	BICD2	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	CEP70	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	DDIT4L	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	PCDHB12	psi-mi:“MI:0915”(physical association)	0.560
PRKAA2	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN9	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN22	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	ZNF426	psi-mi:“MI:0915”(physical association)	0.560
	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN23	PICK1	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZSCAN20	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZNF232	ZNF197	psi-mi:“MI:0914”(association)	0.350

BioGRID (48): ZSCAN23 (Affinity Capture-MS), ZSCAN23 (Affinity Capture-MS), ZSCAN23 (Affinity Capture-MS), ZSCAN23 (Affinity Capture-MS), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (Two-hybrid), ZSCAN23 (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

661 predictions. Top by Δscore:

Variant	Effect	Δscore
6:28443393:GCTCA:G	donor_loss	0.9900
6:28443394:CTCAC:C	donor_loss	0.9900
6:28443395:TCAC:T	donor_loss	0.9900
6:28443396:CA:C	donor_loss	0.9900
6:28443397:A:AC	donor_gain	0.9900
6:28443397:ACCGA:A	donor_loss	0.9900
6:28443398:C:CC	donor_gain	0.9900
6:28435459:CCAAT:C	donor_gain	0.9800
6:28435605:GACC:G	acceptor_loss	0.9800
6:28435606:ACC:A	acceptor_loss	0.9800
6:28435607:CC:C	acceptor_loss	0.9800
6:28435608:C:CG	acceptor_loss	0.9800
6:28435609:T:A	acceptor_loss	0.9800
6:28435853:TCTCA:T	donor_loss	0.9800
6:28435854:CTCA:C	donor_loss	0.9800
6:28435855:TCA:T	donor_loss	0.9800
6:28435856:CAC:C	donor_loss	0.9800
6:28435857:A:C	donor_loss	0.9800
6:28435858:C:CG	donor_loss	0.9800
6:28443360:T:TA	donor_gain	0.9800
6:28443422:C:CT	donor_gain	0.9800
6:28443423:C:CT	donor_gain	0.9600
6:28435095:A:C	acceptor_gain	0.9500
6:28435079:C:CC	acceptor_gain	0.9400
6:28435447:T:TA	donor_gain	0.9400
6:28435510:T:TA	donor_gain	0.9400
6:28443330:AGT:A	donor_gain	0.9400
6:28443351:A:AC	donor_gain	0.9400
6:28443352:C:CC	donor_gain	0.9400
6:28443429:G:C	donor_gain	0.9400

AlphaMissense

2561 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:28434525:G:C	F370L	0.999
6:28434525:G:T	F370L	0.999
6:28434527:A:G	F370L	0.999
6:28434609:A:C	F342L	0.999
6:28434609:A:T	F342L	0.999
6:28434611:A:G	F342L	0.999
6:28434666:G:C	H323Q	0.999
6:28434666:G:T	H323Q	0.999
6:28434693:G:C	F314L	0.999
6:28434693:G:T	F314L	0.999
6:28434695:A:G	F314L	0.999
6:28434777:G:C	F286L	0.999
6:28434777:G:T	F286L	0.999
6:28434779:A:G	F286L	0.999
6:28434861:G:C	F258L	0.999
6:28434861:G:T	F258L	0.999
6:28434863:A:G	F258L	0.999
6:28434508:A:G	L376P	0.998
6:28434526:A:G	F370S	0.998
6:28434570:G:C	H355Q	0.998
6:28434570:G:T	H355Q	0.998
6:28434582:A:C	H351Q	0.998
6:28434582:A:T	H351Q	0.998
6:28434592:A:G	L348P	0.998
6:28434610:A:G	F342S	0.998
6:28434654:G:C	H327Q	0.998
6:28434654:G:T	H327Q	0.998
6:28434668:G:T	H323N	0.998
6:28434580:T:G	Q352P	0.997
6:28434584:G:C	H351D	0.997

dbSNP variants (sampled 300 via entrez): RS1000212999 (6:28442833 G>A,C), RS1000367057 (6:28436188 C>A,T), RS1000398324 (6:28435891 A>G,T), RS1000473775 (6:28443818 C>T), RS1000614825 (6:28443490 A>C), RS1000851060 (6:28435498 C>A,T), RS1000859735 (6:28429438 C>T), RS1001063961 (6:28422068 T>TTA), RS1001090526 (6:28420970 T>C), RS1001137156 (6:28437402 T>C), RS1001196307 (6:28431082 T>C), RS1001229580 (6:28435696 AC>A), RS1001402112 (6:28427739 G>A), RS1001463352 (6:28422586 A>C,G), RS1001710621 (6:28443196 G>A,C)

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

23 associations (top):

Study	Trait	p-value
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_212	Autism spectrum disorder or schizophrenia	5.000000e-14
GCST004521_43	Autism spectrum disorder or schizophrenia	2.000000e-27
GCST004521_7	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004521_77	Autism spectrum disorder or schizophrenia	1.000000e-19
GCST004748_10	Lung cancer	7.000000e-12
GCST004749_75	Lung cancer in ever smokers	2.000000e-09
GCST004946_75	Schizophrenia	5.000000e-36
GCST007323_20	Risk-taking tendency (4-domain principal component model)	1.000000e-08
GCST008573_1	Composite immunoglobulin trait (IgA/IgM)	1.000000e-07
GCST008921_4	Asthma and major depressive disorder	2.000000e-11
GCST010002_50	Refractive error	4.000000e-34
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST90016674_2	Liver iron content	4.000000e-22

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008579	risk-taking behaviour
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Malathion	increases expression	1
Mercuric Chloride	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases expression	1
Antirheumatic Agents	increases expression	1
Zinc Sulfate	decreases expression	1
p-Chloromercuribenzoic Acid	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HD48	HEK293 eGFP-ZSCAN23	Transformed cell line	Female

Clinical trials (associated diseases)

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