ZSCAN20

Summary

ZSCAN20 (zinc finger and SCAN domain containing 20, HGNC:13093) is a protein-coding gene on chromosome 1p35.1, encoding Zinc finger and SCAN domain-containing protein 20 (P17040). 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 7579 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_001377376

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13093
Approved symbol	ZSCAN20
Name	zinc finger and SCAN domain containing 20
Location	1p35.1
Locus type	gene with protein product
Status	Approved
Aliases	KOX29
Ensembl gene	ENSG00000121903
Ensembl biotype	protein_coding
OMIM	611315
Entrez	7579

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 19 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000361328, ENST00000373413, ENST00000480917, ENST00000684572, ENST00000903854, ENST00000903855, ENST00000903856, ENST00000903857, ENST00000948836, ENST00000948837, ENST00000948838, ENST00000948839, ENST00000948840, ENST00000948841, ENST00000948842, ENST00000948843, ENST00000948844, ENST00000948845, ENST00000948846, ENST00000948847

RefSeq mRNA: 5 — MANE Select: NM_001377376 NM_001377376, NM_001377377, NM_001377378, NM_001377379, NM_145238

CCDS: CCDS41300

Canonical transcript exons

ENST00000684572 — 8 exons

Exon	Start	End
ENSE00001435527	33489518	33489602
ENSE00001435769	33489115	33489191
ENSE00001435926	33493187	33493615
ENSE00002722670	33491025	33491702
ENSE00003505215	33488465	33488651
ENSE00003537829	33479179	33479705
ENSE00003917241	33494218	33501643
ENSE00003918394	33472645	33472691

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 81.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.8286 / max 28.7072, expressed in 1179 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2059	1.8286	1179

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	81.27	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.04	gold quality
stromal cell of endometrium	CL:0002255	73.34	gold quality
ventricular zone	UBERON:0003053	72.45	gold quality
ganglionic eminence	UBERON:0004023	71.23	gold quality
calcaneal tendon	UBERON:0003701	70.14	gold quality
islet of Langerhans	UBERON:0000006	69.49	gold quality
corpus callosum	UBERON:0002336	68.20	gold quality
jejunal mucosa	UBERON:0000399	68.10	gold quality
cortical plate	UBERON:0005343	67.78	gold quality
smooth muscle tissue	UBERON:0001135	67.53	gold quality
buccal mucosa cell	CL:0002336	67.37	gold quality
lateral nuclear group of thalamus	UBERON:0002736	67.26	gold quality
jejunum	UBERON:0002115	66.98	gold quality
substantia nigra pars compacta	UBERON:0001965	66.52	gold quality
ventral tegmental area	UBERON:0002691	65.79	gold quality
saphenous vein	UBERON:0007318	65.61	gold quality
cardia of stomach	UBERON:0001162	65.43	gold quality
pericardium	UBERON:0002407	65.40	gold quality
dorsal plus ventral thalamus	UBERON:0001897	65.36	gold quality
inferior vagus X ganglion	UBERON:0005363	65.34	gold quality
subthalamic nucleus	UBERON:0001906	65.31	gold quality
nipple	UBERON:0002030	65.31	gold quality
vena cava	UBERON:0004087	65.18	gold quality
superior surface of tongue	UBERON:0007371	65.06	gold quality
colonic epithelium	UBERON:0000397	65.05	silver quality
substantia nigra pars reticulata	UBERON:0001966	65.03	gold quality
tongue	UBERON:0001723	65.00	gold quality
body of tongue	UBERON:0011876	64.99	gold quality
cerebellar vermis	UBERON:0004720	64.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting ZSCAN20, 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-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-3171	99.49	69.06	776
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-5683	99.36	68.59	2083

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zscan20	ENSMUSG00000061894
rattus_norvegicus	Zscan20	ENSRNOG00000005886

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 20 — P17040 (reviewed: P17040)

Alternative names: Zinc finger protein 31, Zinc finger protein 360, Zinc finger protein KOX29

All UniProt accessions (1): P17040

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 (4)

UniProt ID	Names	Canonical?
P17040-1	1	yes
P17040-2	2
P17040-3	3
P17040-4	4

RefSeq proteins (5): NP_001364305, NP_001364306, NP_001364307, NP_001364308, NP_660281 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001005	SANT/Myb	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily
IPR044822	Myb_DNA-bind_4	Domain

Pfam: PF00096, PF02023, PF13837

UniProt features (27 total): zinc finger region 10, splice variant 5, region of interest 3, sequence conflict 3, compositionally biased region 2, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17040-F1	56.44	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): GGAMTNNNNNTCCY_UNKNOWN, IRF1_Q6, POU3F2_02, CREBP1_01, chr1p35, STAT1_02, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, SMAD_Q6, VDR_Q6, OCT_Q6, LIM_MAMMARY_STEM_CELL_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN

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 (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
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

706 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN20	Q6IQ01	Q6IQ01	572
ZSCAN20	LCN9	Q8WX39	519
ZSCAN20	TTLL11	Q8NHH1	509
ZSCAN20	Q5T8A5	Q5T8A5	492
ZSCAN20	KNDC1	Q76NI1	490
ZSCAN20	CACNA2D3	Q8IZS8	480
ZSCAN20	SACK1E	Q2M2I3	454
ZSCAN20	TRIM62	Q9BVG3	449
ZSCAN20	GUCA1B	Q9UMX6	433
ZSCAN20	SOHLH1	Q5JUK2	424
ZSCAN20	NELL1	Q92832	423
ZSCAN20	KCNT1	Q5JUK3	423
ZSCAN20	GFRA2	O00451	409
ZSCAN20	GPR137C	Q8N3F9	408
ZSCAN20	SIX5	Q8N196	407

IntAct

16 interactions, top by confidence:

A	B	Type	Score
ZSCAN20	SCAND1	psi-mi:“MI:0915”(physical association)	0.550
TGOLN2	DENND11	psi-mi:“MI:0914”(association)	0.530
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZNF397	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZNF396	ZNF24	psi-mi:“MI:0914”(association)	0.530
M		psi-mi:“MI:0914”(association)	0.350
ZNF174	FAM171A2	psi-mi:“MI:0914”(association)	0.350
ZNF232	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZSCAN20	ZNF197	psi-mi:“MI:0914”(association)	0.350
MICU2	ACOX3	psi-mi:“MI:0914”(association)	0.350
TIMM50	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZSCAN20	ZNF24	psi-mi:“MI:0914”(association)	0.350
TGIF2	ZNF213	psi-mi:“MI:0914”(association)	0.350
FHIP1B	MED19	psi-mi:“MI:2364”(proximity)	0.270
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (160): ZSCAN20 (Affinity Capture-MS), ZSCAN20 (Affinity Capture-MS), ZSCAN20 (Affinity Capture-MS), IGKC (Affinity Capture-MS), EPPK1 (Affinity Capture-MS), HMOX1 (Affinity Capture-MS), ZBED9 (Affinity Capture-MS), ZNF232 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZSCAN21 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN4 (Affinity Capture-MS), ZSCAN25 (Affinity Capture-MS), ZNF449 (Affinity Capture-MS), ZKSCAN8 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YX57, A1A5P9, A2A368, A2A9R3, A8MXT2, B2KFW1, O15479, O15480, O15481, O15553, P0C6Y7, P10073, P17040, P25233, P43355, P43356, P43357, P43358, P43360, P43362, P43363, P43364, P43366, Q13342, Q16666, Q4R998, Q5PPP4, Q5RD14, Q6AY37, Q6PCZ4, Q8BQR7, Q8IWY8, Q8IX06, Q8N660, Q8N7X4, Q8TD90, Q96DU7, Q96LZ2, Q96M61, Q99608

Diamond homologs: A0A1W2PQ72, B2KFW1, P17040, Q63HK3, Q8IWY8, Q9NX65, A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	127
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1329 predictions. Top by Δscore:

Variant	Effect	Δscore
1:33488647:GAGTG:G	donor_gain	1.0000
1:33488649:GTG:G	donor_gain	1.0000
1:33489113:A:AG	acceptor_gain	1.0000
1:33489114:G:GA	acceptor_gain	1.0000
1:33489114:GCT:G	acceptor_gain	1.0000
1:33489188:CCAGG:C	donor_loss	1.0000
1:33489189:CAGGT:C	donor_loss	1.0000
1:33489190:AGGT:A	donor_loss	1.0000
1:33489192:G:C	donor_loss	1.0000
1:33489193:T:G	donor_loss	1.0000
1:33494212:TTTCA:T	acceptor_loss	1.0000
1:33494213:TTCA:T	acceptor_loss	1.0000
1:33494214:TCAG:T	acceptor_loss	1.0000
1:33494215:CAGGT:C	acceptor_loss	1.0000
1:33494217:G:GC	acceptor_loss	1.0000
1:33479178:GA:G	acceptor_gain	0.9900
1:33488460:TGTA:T	acceptor_loss	0.9900
1:33488461:GTAG:G	acceptor_loss	0.9900
1:33488462:TAGG:T	acceptor_loss	0.9900
1:33488463:A:AG	acceptor_gain	0.9900
1:33488463:AG:A	acceptor_gain	0.9900
1:33488463:AGG:A	acceptor_gain	0.9900
1:33488464:G:GG	acceptor_gain	0.9900
1:33488464:GG:G	acceptor_gain	0.9900
1:33488464:GGG:G	acceptor_gain	0.9900
1:33488464:GGGA:G	acceptor_gain	0.9900
1:33488648:AGTG:A	donor_gain	0.9900
1:33488649:GTGG:G	donor_gain	0.9900
1:33488649:GTGGT:G	donor_loss	0.9900
1:33488650:TGGT:T	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000159162 (1:33498403 G>A), RS1000169805 (1:33471750 T>A,G), RS1000208654 (1:33490845 T>A), RS1000417249 (1:33474835 T>C), RS1000720286 (1:33473402 C>G,T), RS1000751741 (1:33473106 A>G), RS1000983040 (1:33480320 G>A,C), RS1001360941 (1:33473209 T>C), RS1001395778 (1:33476979 C>T), RS1001511091 (1:33490983 C>A,G), RS1001620163 (1:33480437 CA>C), RS1001725658 (1:33497348 A>G), RS1001831530 (1:33499795 T>C), RS1001874230 (1:33489108 T>C), RS1001951449 (1:33482272 G>C)

Disease associations

OMIM: gene MIM:611315 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST003063_1	Neuropathic pain in type 2 diabetes	4.000000e-07
GCST003063_2	Neuropathic pain in type 2 diabetes	3.000000e-07
GCST005986_1	Blood urea nitrogen levels	9.000000e-09
GCST006586_42	Urinary albumin excretion	9.000000e-11
GCST009640_2	Urinary albumin-to-creatinine ratio	4.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005762	neuropathic pain
EFO:0004285	albuminuria
EFO:0007778	urinary albumin to creatinine ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	3
Tobacco Smoke Pollution	increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
cupric oxide	increases expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	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
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Demecolcine	increases expression	1
Bucladesine	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Medroxyprogesterone Acetate	affects cotreatment, increases expression	1
Acrylamide	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_XW91	HEK293 eGFP-ZSCAN20	Transformed cell line	Female

Clinical trials (associated diseases)

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