ZSCAN22

Summary

ZSCAN22 (zinc finger and SCAN domain containing 22, HGNC:4929) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 22 (P10073). 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 342945 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_181846

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4929
Approved symbol	ZSCAN22
Name	zinc finger and SCAN domain containing 22
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000182318
Ensembl biotype	protein_coding
OMIM	165260
Entrez	342945

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000329665, ENST00000850584, ENST00000904370, ENST00000904371, ENST00000904372, ENST00000904373, ENST00000904374

RefSeq mRNA: 3 — MANE Select: NM_181846 NM_001321116, NM_001321117, NM_181846

CCDS: CCDS12975

Canonical transcript exons

ENST00000329665 — 3 exons

Exon	Start	End
ENSE00001333334	58334752	58335205
ENSE00001333335	58326994	58327114
ENSE00002284614	58338254	58342332

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 82.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.2776 / max 135.8130, expressed in 1552 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177828	2.8841	1475
208953	0.3935	186

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.64	gold quality
ileal mucosa	UBERON:0000331	77.71	gold quality
tibialis anterior	UBERON:0001385	76.64	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.39	gold quality
stromal cell of endometrium	CL:0002255	71.61	gold quality
cerebellar vermis	UBERON:0004720	71.33	gold quality
pancreatic ductal cell	CL:0002079	70.88	silver quality
granulocyte	CL:0000094	69.90	gold quality
islet of Langerhans	UBERON:0000006	69.89	gold quality
cortical plate	UBERON:0005343	68.88	gold quality
upper arm skin	UBERON:0004263	68.61	gold quality
ganglionic eminence	UBERON:0004023	68.59	gold quality
lower esophagus mucosa	UBERON:0035834	67.17	gold quality
deltoid	UBERON:0001476	66.89	silver quality
right lobe of liver	UBERON:0001114	66.38	gold quality
ventricular zone	UBERON:0003053	66.20	gold quality
cerebellar cortex	UBERON:0002129	65.96	gold quality
cardiac muscle of right atrium	UBERON:0003379	65.87	gold quality
cerebellar hemisphere	UBERON:0002245	65.86	gold quality
hindlimb stylopod muscle	UBERON:0004252	65.51	gold quality
right hemisphere of cerebellum	UBERON:0014890	65.46	gold quality
right adrenal gland	UBERON:0001233	65.25	gold quality
smooth muscle tissue	UBERON:0001135	65.20	gold quality
pituitary gland	UBERON:0000007	65.15	gold quality
skin of leg	UBERON:0001511	65.05	gold quality
right adrenal gland cortex	UBERON:0035827	64.99	gold quality
adenohypophysis	UBERON:0002196	64.96	gold quality
left adrenal gland	UBERON:0001234	64.82	gold quality
cerebellum	UBERON:0002037	64.80	gold quality
right coronary artery	UBERON:0001625	64.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

96 targeting ZSCAN22, 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-4533	100.00	69.48	2758
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-5002-5P	99.76	70.84	1763

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zscan22	ENSMUSG00000054715
rattus_norvegicus	Zscan22	ENSRNOG00000031113

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), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), 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 22 — P10073 (reviewed: P10073)

Alternative names: Krueppel-related zinc finger protein 2, Protein HKR2, Zinc finger protein 50

All UniProt accessions (1): P10073

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 (3): NP_001308045, NP_001308046, NP_862829* (*=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 (16 total): zinc finger region 8, region of interest 2, compositionally biased region 2, chain 1, domain 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P10073-F1	69.05	0.39

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 (2): 9, 443

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GTGCCTT_MIR506, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ZWANG_DOWN_BY_2ND_EGF_PULSE, RB_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FEV_TARGET_GENES, H1_6_TARGET_GENES, HES4_TARGET_GENES, NFE2L1_TARGET_GENES, SALL4_TARGET_GENES, TEAD2_TARGET_GENES, ZNF766_TARGET_GENES, ZNF8_TARGET_GENES

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): 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)

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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

570 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN22	MYCL	P12524	498
ZSCAN22	MYCN	P04198	431
ZSCAN22	PRR19	A6NJB7	418
ZSCAN22	ZSCAN21	Q9Y5A6	396
ZSCAN22	NRAS	P01111	390
ZSCAN22	CCDC97	Q96F63	370
ZSCAN22	ZSWIM5	Q9P217	348
ZSCAN22	A0A0A6YYG8	A0A0A6YYG8	336
ZSCAN22	ERBB2	P04626	323
ZSCAN22	FAM8A1	Q9UBU6	315
ZSCAN22	ZNF750	Q32MQ0	311
ZSCAN22	EGFR	P00533	311
ZSCAN22	APOE	P02649	305
ZSCAN22	ALDH16A1	Q8IZ83	296
ZSCAN22	ZBTB48	P10074	289

IntAct

156 interactions, top by confidence:

A	B	Type	Score
ZSCAN22	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.800
ZSCAN32	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.800
PGBD1	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.790
ZSCAN22	PGBD1	psi-mi:“MI:0915”(physical association)	0.790
ZSCAN22	ZNF496	psi-mi:“MI:0915”(physical association)	0.780
ZNF496	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.780
ZSCAN22	SCAND1	psi-mi:“MI:0915”(physical association)	0.760
ZSCAN22	ZNF446	psi-mi:“MI:0915”(physical association)	0.720
ZNF446	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.720
ZNF483	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN22	ZNF483	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (46): ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Affinity Capture-MS), ZSCAN22 (Affinity Capture-MS), ZSCAN22 (Two-hybrid), SCAND1 (Affinity Capture-MS), ZSCAN22 (Affinity Capture-MS), ZSCAN22 (Affinity Capture-MS), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid), ZSCAN22 (Two-hybrid)

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: 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

792 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58327444:G:GG	donor_gain	0.9800
19:58327514:A:G	donor_gain	0.9800
19:58335201:GAGAG:G	donor_gain	0.9800
19:58327441:G:GT	donor_gain	0.9700
19:58327507:A:G	donor_gain	0.9700
19:58335203:GAG:G	donor_gain	0.9700
19:58335267:G:GT	donor_gain	0.9700
19:58334748:GC:G	acceptor_loss	0.9600
19:58334749:CAG:C	acceptor_loss	0.9600
19:58334751:G:GC	acceptor_loss	0.9600
19:58335157:G:GT	donor_gain	0.9600
19:58327485:G:GT	donor_gain	0.9500
19:58334750:A:AG	acceptor_gain	0.9500
19:58334751:G:GG	acceptor_gain	0.9500
19:58335202:AGAGG:A	donor_loss	0.9500
19:58335204:AGG:A	donor_loss	0.9500
19:58335205:GGTAA:G	donor_loss	0.9500
19:58335207:T:G	donor_loss	0.9500
19:58327521:G:GG	donor_gain	0.9400
19:58327441:GGA:G	donor_gain	0.9300
19:58327442:GAG:G	donor_gain	0.9300
19:58327443:A:T	donor_gain	0.9300
19:58335208:A:T	donor_loss	0.9200
19:58335260:G:GT	donor_gain	0.9100
19:58327400:C:CG	donor_gain	0.9000
19:58327442:GA:G	donor_gain	0.9000
19:58327454:G:GT	donor_gain	0.9000
19:58334751:GGCCC:G	acceptor_gain	0.9000
19:58335496:G:GG	donor_gain	0.9000
19:58327449:T:A	donor_gain	0.8900

AlphaMissense

3212 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:58338763:T:C	F305L	0.999
19:58338765:C:A	F305L	0.999
19:58338765:C:G	F305L	0.999
19:58338847:T:C	F333L	0.999
19:58338849:C:A	F333L	0.999
19:58338849:C:G	F333L	0.999
19:58338931:T:C	F361L	0.999
19:58338933:C:A	F361L	0.999
19:58338933:C:G	F361L	0.999
19:58339015:T:C	F389L	0.999
19:58339017:C:A	F389L	0.999
19:58339017:C:G	F389L	0.999
19:58339099:T:C	F417L	0.999
19:58339101:C:A	F417L	0.999
19:58339101:C:G	F417L	0.999
19:58339183:T:C	F445L	0.999
19:58339185:T:A	F445L	0.999
19:58339185:T:G	F445L	0.999
19:58339267:T:C	F473L	0.999
19:58339269:C:A	F473L	0.999
19:58339269:C:G	F473L	0.999
19:58338876:C:A	H342Q	0.998
19:58338876:C:G	H342Q	0.998
19:58338874:C:G	H342D	0.997
19:58338888:T:A	H346Q	0.997
19:58338888:T:G	H346Q	0.997
19:58338950:T:C	L367P	0.997
19:58338960:C:A	H370Q	0.997
19:58338960:C:G	H370Q	0.997
19:58339034:T:C	L395P	0.997

dbSNP variants (sampled 300 via entrez): RS1000381162 (19:58337363 C>G,T), RS1000409987 (19:58330498 T>A), RS1000698980 (19:58334933 A>T), RS1000958073 (19:58341124 A>G), RS1001178283 (19:58338663 C>T), RS1001407962 (19:58332161 G>A), RS1001465545 (19:58325761 T>G), RS1001695362 (19:58332035 G>A), RS1002216867 (19:58339950 C>T), RS1002238907 (19:58331513 C>T), RS1002291474 (19:58333546 A>T), RS1002467957 (19:58327051 G>A,C,T), RS1002471045 (19:58338382 T>C), RS1002818136 (19:58333796 T>C,G), RS1002852298 (19:58337020 T>C)

Disease associations

OMIM: gene MIM:165260 | 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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	increases expression	1
urushiol	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
Sunitinib	decreases expression	1
Benzene	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases methylation	1
Lithium Chloride	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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