ZSCAN30

Summary

ZSCAN30 (zinc finger and SCAN domain containing 30, HGNC:33517) is a protein-coding gene on chromosome 18q12.2, encoding Zinc finger and SCAN domain-containing protein 30 (Q86W11). 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 100101467 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001112734

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33517
Approved symbol	ZSCAN30
Name	zinc finger and SCAN domain containing 30
Location	18q12.2
Locus type	gene with protein product
Status	Approved
Aliases	ZNF917
Ensembl gene	ENSG00000186814
Ensembl biotype	protein_coding
Entrez	100101467

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000333206, ENST00000420878, ENST00000588448, ENST00000588832, ENST00000589178, ENST00000590777, ENST00000592211, ENST00000592278, ENST00000592598, ENST00000601405, ENST00000610712, ENST00000874229, ENST00000925335

RefSeq mRNA: 3 — MANE Select: NM_001112734 NM_001112734, NM_001166012, NM_001288711

CCDS: CCDS42427, CCDS74207

Canonical transcript exons

ENST00000333206 — 4 exons

Exon	Start	End
ENSE00001335650	35263513	35263657
ENSE00002764019	35290084	35290229
ENSE00002994806	35263945	35264455
ENSE00003720928	35251062	35254381

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 93.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.3103 / max 78.7643, expressed in 1635 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
171643	5.9085	1616
171642	0.2143	97
171641	0.1875	88

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	93.33	gold quality
corpus callosum	UBERON:0002336	90.40	gold quality
cerebellar hemisphere	UBERON:0002245	90.22	gold quality
cerebellar cortex	UBERON:0002129	90.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.10	gold quality
cerebellum	UBERON:0002037	89.61	gold quality
pancreatic ductal cell	CL:0002079	89.35	silver quality
medial globus pallidus	UBERON:0002477	87.97	gold quality
deltoid	UBERON:0001476	87.87	silver quality
tendon of biceps brachii	UBERON:0008188	87.80	silver quality
cardiac atrium	UBERON:0002081	87.69	gold quality
right atrium auricular region	UBERON:0006631	87.62	gold quality
globus pallidus	UBERON:0001875	87.61	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.57	silver quality
ganglionic eminence	UBERON:0004023	87.46	gold quality
upper arm skin	UBERON:0004263	87.19	gold quality
gastrocnemius	UBERON:0001388	87.07	gold quality
epithelial cell of pancreas	CL:0000083	86.94	silver quality
cerebellar vermis	UBERON:0004720	86.85	silver quality
pituitary gland	UBERON:0000007	86.84	gold quality
tibial nerve	UBERON:0001323	86.83	gold quality
kidney epithelium	UBERON:0004819	86.78	silver quality
subthalamic nucleus	UBERON:0001906	86.72	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.70	gold quality
muscle of leg	UBERON:0001383	86.62	gold quality
adenohypophysis	UBERON:0002196	86.62	gold quality
right lobe of thyroid gland	UBERON:0001119	86.46	gold quality
apex of heart	UBERON:0002098	86.45	gold quality
quadriceps femoris	UBERON:0001377	86.44	silver quality
colonic epithelium	UBERON:0000397	86.25	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.51
E-GEOD-111727	no	517.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

96 targeting ZSCAN30, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-548AZ-3P	99.82	70.56	3549

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Zscan30	ENSRNOG00000030131

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), 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 30 — Q86W11 (reviewed: Q86W11)

Alternative names: ZNF-WYM, Zinc finger protein 397 opposite strand, Zinc finger protein 397OS

All UniProt accessions (8): A0A0C4DGV0, C9JCM2, Q86W11, K7EPB0, K7ERA9, M0QZC3, M0QZP2, M0R1Y0

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 ID	Names	Canonical?
Q86W11-1	1	yes
Q86W11-3	2

RefSeq proteins (3): NP_001106205, NP_001159484, NP_001275640 (=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 (13 total): zinc finger region 7, splice variant 2, chain 1, domain 1, sequence variant 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86W11-F1	64.90	0.34

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 (1): 197

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): chr18q12, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HORIUCHI_WTAP_TARGETS_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, DLX4_TARGET_GENES, E2F2_TARGET_GENES, GLI3_TARGET_GENES, MAFG_TARGET_GENES, OVOL3_TARGET_GENES, SNIP1_TARGET_GENES, SUPT16H_TARGET_GENES, TOP2B_TARGET_GENES, ZFP3_TARGET_GENES, ZNF257_TARGET_GENES

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), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (2): nucleoplasm (GO:0005654), 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
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nuclear lumen	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN30	R3HDM2	Q9Y2K5	560
ZSCAN30	C2CD4D	B7Z1M9	480
ZSCAN30	PAQR9	Q6ZVX9	445
ZSCAN30	OR2B11	Q5JQS5	435
ZSCAN30	GAB4	Q2WGN9	431
ZSCAN30	ZBED5	Q49AG3	431
ZSCAN30	ECSCR	Q19T08	428
ZSCAN30	ARHGEF35	A5YM69	419
ZSCAN30	MPRIP	Q6WCQ1	394
ZSCAN30	RGPD5	Q99666	393
ZSCAN30	CCDC12	Q8WUD4	365
ZSCAN30	NPAS1	Q99742	365
ZSCAN30	ZMYM5	Q9UJ78	363
ZSCAN30	VSIG8	P0DPA2	358
ZSCAN30	EOLA1	Q8TE69	353

IntAct

135 interactions, top by confidence:

A	B	Type	Score
ZSCAN30	DLG1	psi-mi:“MI:0915”(physical association)	0.610
ZSCAN30	DLG1	psi-mi:“MI:0407”(direct interaction)	0.610
ZSCAN30	ZNF446	psi-mi:“MI:0915”(physical association)	0.560
RNPS1	ZSCAN30	psi-mi:“MI:0915”(physical association)	0.560
FRS3	ZSCAN30	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN30	ZKSCAN4	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZNF397	ZNF197	psi-mi:“MI:0914”(association)	0.530
MAGI2	ZSCAN30	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
MAST2	ZSCAN30	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	MAGI1	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	LNX2	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440
SNX27	ZSCAN30	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	GORASP2	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	TAMALIN	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	SYNJ2BP	psi-mi:“MI:0407”(direct interaction)	0.440
ZSCAN30	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (24): ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZSCAN30 (Affinity Capture-MS), ZNF446 (Two-hybrid), ZSCAN30 (Two-hybrid), ZSCAN30 (Two-hybrid), ZKSCAN4 (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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 91 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
Ras activation upon Ca2+ influx through NMDA receptor	5	49.2×	2e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	46.9×	2e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	46.9×	2e-06
Assembly and cell surface presentation of NMDA receptors	10	43.8×	2e-12
Dopamine Neurotransmitter Release Cycle	5	42.8×	3e-06
Long-term potentiation	5	41.0×	4e-06
Neurexins and neuroligins	11	37.3×	1e-12
Protein-protein interactions at synapses	7	32.0×	2e-07

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	9	58.8×	9e-12
protein localization to synapse	6	51.6×	3e-07
receptor clustering	6	42.1×	8e-07
regulation of postsynaptic membrane neurotransmitter receptor levels	5	27.9×	7e-05
cell-cell adhesion	9	10.3×	2e-05
protein-containing complex assembly	8	10.2×	8e-05
chemical synaptic transmission	7	6.1×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1088 predictions. Top by Δscore:

Variant	Effect	Δscore
18:35263942:TA:T	donor_loss	1.0000
18:35263944:C:A	donor_loss	1.0000
18:35264451:CGCTC:C	acceptor_gain	1.0000
18:35254379:CAT:C	acceptor_gain	0.9900
18:35254382:C:CC	acceptor_gain	0.9900
18:35263943:A:AC	donor_gain	0.9900
18:35263944:C:CC	donor_gain	0.9900
18:35264453:CTC:C	acceptor_gain	0.9900
18:35264453:CTCCT:C	acceptor_loss	0.9900
18:35264454:TC:T	acceptor_gain	0.9900
18:35264455:CC:C	acceptor_gain	0.9900
18:35264456:C:CG	acceptor_loss	0.9900
18:35264457:T:C	acceptor_loss	0.9900
18:35267474:AC:A	donor_gain	0.9900
18:35267475:CC:C	donor_gain	0.9900
18:35290082:AC:A	donor_gain	0.9900
18:35290083:CC:C	donor_gain	0.9900
18:35254377:GCCAT:G	acceptor_gain	0.9800
18:35254378:CCAT:C	acceptor_gain	0.9800
18:35254378:CCATC:C	acceptor_gain	0.9800
18:35254379:CATC:C	acceptor_gain	0.9800
18:35254379:CATCT:C	acceptor_gain	0.9800
18:35254380:AT:A	acceptor_gain	0.9800
18:35254380:ATCTA:A	acceptor_gain	0.9800
18:35254381:TCTA:T	acceptor_loss	0.9800
18:35254382:C:T	acceptor_loss	0.9800
18:35254383:T:C	acceptor_loss	0.9800
18:35254388:A:AC	acceptor_gain	0.9800
18:35254388:A:C	acceptor_gain	0.9800
18:35255503:A:C	donor_gain	0.9800

AlphaMissense

3276 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:35253501:A:C	F478L	0.999
18:35253501:A:T	F478L	0.999
18:35253503:A:G	F478L	0.999
18:35253585:G:C	F450L	0.999
18:35253585:G:T	F450L	0.999
18:35253587:A:G	F450L	0.999
18:35253753:G:C	F394L	0.999
18:35253753:G:T	F394L	0.999
18:35253755:A:G	F394L	0.999
18:35253837:G:C	F366L	0.999
18:35253837:G:T	F366L	0.999
18:35253839:A:G	F366L	0.999
18:35253921:G:C	F338L	0.999
18:35253921:G:T	F338L	0.999
18:35253923:A:G	F338L	0.999
18:35253558:G:C	H459Q	0.998
18:35253558:G:T	H459Q	0.998
18:35253560:G:C	H459D	0.998
18:35253669:A:C	F422L	0.998
18:35253669:A:T	F422L	0.998
18:35253671:A:G	F422L	0.998
18:35253812:G:C	H375D	0.998
18:35254005:A:C	F310L	0.998
18:35254005:A:T	F310L	0.998
18:35254007:A:G	F310L	0.998
18:35253546:G:C	H463Q	0.997
18:35253546:G:T	H463Q	0.997
18:35253568:A:G	L456P	0.997
18:35253642:A:C	H431Q	0.997
18:35253642:A:T	H431Q	0.997

dbSNP variants (sampled 300 via entrez): RS1000012357 (18:35267157 C>G), RS1000014415 (18:35251455 CAAAG>C), RS1000157606 (18:35291902 G>C), RS1000209521 (18:35292223 G>A), RS1000326648 (18:35285061 G>A), RS1000373211 (18:35277309 G>C), RS1000559759 (18:35262639 A>T), RS1000663655 (18:35255443 G>A), RS1000667402 (18:35284770 G>A), RS1000859347 (18:35272443 C>A), RS1000878578 (18:35290062 T>G), RS1000971688 (18:35272955 G>A,C), RS1001020679 (18:35268136 C>T), RS1001234507 (18:35259216 T>C), RS1001297989 (18:35252047 A>G)

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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment	3
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
titanium dioxide	increases expression	1
sodium arsenite	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Lead	increases expression	1
Silicon Dioxide	decreases expression, increases methylation	1
Urethane	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Magnetite Nanoparticles	increases methylation	1

Clinical trials (associated diseases)

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