ZSCAN1

Summary

ZSCAN1 (zinc finger and SCAN domain containing 1, HGNC:23712) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 1 (Q8NBB4). 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 chromatin.

Source: NCBI Gene 284312 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_182572

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23712
Approved symbol	ZSCAN1
Name	zinc finger and SCAN domain containing 1
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33779, ZNF915
Ensembl gene	ENSG00000152467
Ensembl biotype	protein_coding
OMIM	620026
Entrez	284312

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000282326, ENST00000391700, ENST00000601162

RefSeq mRNA: 1 — MANE Select: NM_182572 NM_182572

CCDS: CCDS12969

Canonical transcript exons

ENST00000282326 — 6 exons

Exon	Start	End
ENSE00001183770	58037728	58038206
ENSE00001251640	58053429	58054631
ENSE00001251651	58052490	58052628
ENSE00001251668	58040450	58040544
ENSE00001251687	58035970	58036011
ENSE00001251701	58034025	58034161

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 85.39.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8456 / max 61.2894, expressed in 434 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177810	1.2604	376
177809	0.5853	249

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	85.39	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.76	gold quality
pituitary gland	UBERON:0000007	81.74	gold quality
right uterine tube	UBERON:0001302	81.50	gold quality
hypothalamus	UBERON:0001898	77.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.01	silver quality
left lobe of thyroid gland	UBERON:0001120	75.64	gold quality
Brodmann (1909) area 9	UBERON:0013540	75.56	gold quality
anterior cingulate cortex	UBERON:0009835	75.50	gold quality
right frontal lobe	UBERON:0002810	74.89	gold quality
prefrontal cortex	UBERON:0000451	74.45	gold quality
left testis	UBERON:0004533	74.27	gold quality
right lobe of thyroid gland	UBERON:0001119	73.88	gold quality
right testis	UBERON:0004534	73.86	gold quality
thyroid gland	UBERON:0002046	73.32	gold quality
amygdala	UBERON:0001876	73.04	gold quality
nucleus accumbens	UBERON:0001882	72.46	gold quality
caudate nucleus	UBERON:0001873	71.49	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.36	gold quality
putamen	UBERON:0001874	71.25	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	71.14	gold quality
testis	UBERON:0000473	70.82	gold quality
ventricular zone	UBERON:0003053	70.65	gold quality
cerebellar hemisphere	UBERON:0002245	70.63	gold quality
cerebellar cortex	UBERON:0002129	70.58	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	70.32	gold quality
neocortex	UBERON:0001950	69.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	68.96	gold quality
cortical plate	UBERON:0005343	68.60	gold quality
cerebellum	UBERON:0002037	68.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting ZSCAN1, 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-548AW	99.99	72.57	3559
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-3136-5P	98.53	67.68	793
HSA-MIR-4439	98.53	67.53	793
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-4669	97.94	62.71	224
HSA-MIR-3657	96.33	66.29	608
HSA-MIR-4513	95.04	67.06	727
HSA-MIR-6855-3P	95.04	66.57	725
HSA-MIR-5588-3P	94.96	65.59	500
HSA-MIR-764	94.16	64.85	656

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	plagx	ENSDARG00000036855
danio_rerio	ovol1a	ENSDARG00000076472
danio_rerio	plagl2	ENSDARG00000076657
danio_rerio	ovol1b	ENSDARG00000078256
drosophila_melanogaster	hb	FBGN0001180
drosophila_melanogaster	CG12391	FBGN0033581
caenorhabditis_elegans		WBGENE00001824
caenorhabditis_elegans		WBGENE00003033
caenorhabditis_elegans		WBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZSCAN18 (ENSG00000121413), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN29 (ENSG00000140265), ZSCAN32 (ENSG00000140987), 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 1 — Q8NBB4 (reviewed: Q8NBB4)

All UniProt accessions (2): Q8NBB4, A0A0C4DGR0

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NBB4-1	1	yes
Q8NBB4-2	2

RefSeq proteins (1): NP_872378* (*=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
IPR050916	SCAN-C2H2_zinc_finger	Family

Pfam: PF00096, PF02023

UniProt features (15 total): region of interest 5, zinc finger region 3, splice variant 2, sequence conflict 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBB4-F1	60.15	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MARTENS_TRETINOIN_RESPONSE_UP, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR153_5P, MIR6853_3P, MIR3136_5P, MIR4439, MANNO_MIDBRAIN_NEUROTYPES_HRGL3, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, GSE29614_CTRL_VS_TIV_FLU_VACCINE_PBMC_2007_UP

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 (2): chromatin (GO:0000785), 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
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

908 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN1	PLVAP	Q9BX97	712
ZSCAN1	MAZ	P56270	658
ZSCAN1	TGFB1	P01137	574
ZSCAN1	USF1	P22415	537
ZSCAN1	NKX2-5	P52952	502
ZSCAN1	GATA1	P15976	486
ZSCAN1	POU2F1	P14859	478
ZSCAN1	ZNF174	Q15697	463
ZSCAN1	ZNF202	O95125	459
ZSCAN1	INSM1	Q01101	453
ZSCAN1	POU3F2	P20265	451
ZSCAN1	RUBCNL	Q9H714	445
ZSCAN1	KLF6	Q99612	443
ZSCAN1	SMAD3	P84022	442
ZSCAN1	EIF2AK1	Q9BQI3	435

IntAct

47 interactions, top by confidence:

A	B	Type	Score
PPL	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN1	GOPC	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN1	PPL	psi-mi:“MI:0915”(physical association)	0.560
GOPC	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN1	SH2D2A	psi-mi:“MI:0915”(physical association)	0.490
SH2D2A	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.490
CDK6	ZSCAN1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
ZNF263	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
SSX3	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
TRIM31	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
ERCC3	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
SNW1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
ZKSCAN5	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
CNOT6L	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
ZNF396	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
ZSCAN1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
GTF2E1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
GTF2H1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
NPAS2	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
MED31	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
PLRG1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
POLR2B	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
POLR2D	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
POLR2E	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
PPARG	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
ZNF407	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
TBX20	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370
RFC1	ZSCAN1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (74): ZSCAN1 (Two-hybrid), ZSCAN1 (Two-hybrid), ZNF24 (Affinity Capture-MS), ZSCAN25 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), ZNF174 (Affinity Capture-MS), ZNF496 (Affinity Capture-MS), ZSCAN18 (Affinity Capture-MS), PM20D2 (Affinity Capture-MS), MZF1 (Affinity Capture-MS), PGBD1 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZSCAN1 (Two-hybrid), ZSCAN18 (Affinity Capture-MS), ZNF174 (Affinity Capture-MS)

ESM2 similar proteins: A1YGK1, A2T7E6, A4D1S0, A9YTQ3, B1WBS3, I7HJS4, O43593, O43918, O60304, O75593, O95201, P0C6A0, P0C7X2, P97609, Q2MHN3, Q3B7M4, Q3SY56, Q3U133, Q58DK7, Q5JPB2, Q5SXI5, Q5T619, Q61645, Q6KAU7, Q6NUN9, Q6ZMS7, Q76NI1, Q7Z6P3, Q8BZ34, Q8BZW2, Q8CGW9, Q8IWN7, Q8IXT2, Q8IZ20, Q8NBB4, Q8NDX1, Q8NHY3, Q91X45, Q96PX9, Q99558

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFC1, 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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 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:

Pathway	Partners	Fold	FDR
RNA Pol II CTD phosphorylation and interaction with CE during HIV infection	5	70.3×	1e-07
RNA Pol II CTD phosphorylation and interaction with CE	5	70.3×	1e-07
mRNA Capping	5	65.6×	2e-07
Formation of the Early Elongation Complex	5	57.9×	2e-07
Formation of the HIV-1 Early Elongation Complex	5	57.9×	2e-07
HIV Transcription Initiation	7	56.3×	9e-10
RNA Polymerase II HIV Promoter Escape	7	56.3×	9e-10
RNA Polymerase II Promoter Escape	7	56.3×	9e-10

GO biological processes:

GO term	Partners	Fold	FDR
transcription initiation at RNA polymerase II promoter	6	57.6×	2e-07
transcription by RNA polymerase II	8	14.5×	9e-06
DNA repair	6	9.8×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1264 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58038203:G:GT	donor_gain	1.0000
19:58038204:A:T	donor_gain	1.0000
19:58040445:CACA:C	acceptor_loss	1.0000
19:58040447:C:G	acceptor_gain	1.0000
19:58040447:CA:C	acceptor_loss	1.0000
19:58040448:A:AC	acceptor_loss	1.0000
19:58040448:A:AG	acceptor_gain	1.0000
19:58040449:G:GC	acceptor_gain	1.0000
19:58040449:GT:G	acceptor_gain	1.0000
19:58040449:GTT:G	acceptor_gain	1.0000
19:58040449:GTTC:G	acceptor_gain	1.0000
19:58040449:GTTCT:G	acceptor_gain	1.0000
19:58040540:CGCAG:C	donor_loss	1.0000
19:58040542:CAGG:C	donor_loss	1.0000
19:58040543:AGGTG:A	donor_loss	1.0000
19:58040544:GGTGA:G	donor_loss	1.0000
19:58040546:T:A	donor_loss	1.0000
19:58052489:GGC:G	acceptor_gain	1.0000
19:58053427:AG:A	acceptor_gain	1.0000
19:58053428:GG:G	acceptor_gain	1.0000
19:58034157:GCGCG:G	donor_gain	0.9900
19:58034158:CGCGG:C	donor_loss	0.9900
19:58034159:GCG:G	donor_gain	0.9900
19:58034162:G:GG	donor_gain	0.9900
19:58034162:GTGA:G	donor_loss	0.9900
19:58034163:T:A	donor_loss	0.9900
19:58034164:GA:G	donor_loss	0.9900
19:58035959:T:G	acceptor_gain	0.9900
19:58036061:G:GT	donor_gain	0.9900
19:58037099:G:GT	donor_gain	0.9900

AlphaMissense

2653 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:58038183:T:C	L116P	0.999
19:58053725:T:C	F301L	0.999
19:58053727:C:A	F301L	0.999
19:58053727:C:G	F301L	0.999
19:58053809:T:C	F329L	0.999
19:58053810:T:C	F329S	0.999
19:58053811:C:A	F329L	0.999
19:58053811:C:G	F329L	0.999
19:58053989:T:C	F389L	0.999
19:58053991:C:A	F389L	0.999
19:58053991:C:G	F389L	0.999
19:58038084:T:C	L83P	0.998
19:58038093:T:C	F86S	0.998
19:58038171:T:C	L112P	0.998
19:58053726:T:C	F301S	0.998
19:58053788:T:C	C322R	0.998
19:58053968:T:C	C382R	0.998
19:58053990:T:C	F389S	0.998
19:58054008:T:C	L395P	0.998
19:58054016:C:G	H398D	0.998
19:58054018:C:A	H398Q	0.998
19:58054018:C:G	H398Q	0.998
19:58038012:T:C	L59P	0.997
19:58038075:T:C	L80P	0.997
19:58038092:T:C	F86L	0.997
19:58038094:C:A	F86L	0.997
19:58038094:C:G	F86L	0.997
19:58038105:T:C	L90P	0.997
19:58053744:T:C	F307S	0.997
19:58053752:C:G	H310D	0.997

dbSNP variants (sampled 300 via entrez): RS1000214354 (19:58040308 T>A), RS1000263351 (19:58034352 C>A), RS1000336971 (19:58045009 C>G), RS1000375428 (19:58035958 A>C,G), RS1000604168 (19:58035670 G>A), RS1000654806 (19:58035951 T>C), RS1000662220 (19:58045420 G>A), RS1000687422 (19:58045155 C>T), RS1000699435 (19:58052331 C>T), RS1000773036 (19:58052485 T>C), RS1000847773 (19:58039387 C>T), RS1001194724 (19:58054979 G>A), RS1001283556 (19:58049306 T>A), RS1001288476 (19:58055012 C>T), RS1001447916 (19:58049912 G>T)

Disease associations

OMIM: gene MIM:620026 | 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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
Methapyrilene	decreases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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