ZSCAN32

Summary

ZSCAN32 (zinc finger and SCAN domain containing 32, HGNC:20812) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger and SCAN domain-containing protein 32 (Q9NX65). May be involved in transcriptional regulation.

Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 54925 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_001284527

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20812
Approved symbol	ZSCAN32
Name	zinc finger and SCAN domain containing 32
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20417
Ensembl gene	ENSG00000140987
Ensembl biotype	protein_coding
Entrez	54925

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 16 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000304926, ENST00000396852, ENST00000422427, ENST00000439568, ENST00000571285, ENST00000571906, ENST00000573719, ENST00000573830, ENST00000574940, ENST00000575350, ENST00000576500, ENST00000618425, ENST00000853179, ENST00000853180, ENST00000853181, ENST00000853182, ENST00000939891, ENST00000970393

RefSeq mRNA: 11 — MANE Select: NM_001284527 NM_001284527, NM_001284528, NM_001284529, NM_001324340, NM_001324341, NM_001324342, NM_001324343, NM_001324344, NM_001324345, NM_001324346, NM_017810

CCDS: CCDS10503, CCDS66920, CCDS66921

Canonical transcript exons

ENST00000396852 — 7 exons

Exon	Start	End
ENSE00001228145	3382085	3383711
ENSE00002253096	3397192	3397744
ENSE00002270439	3400945	3401004
ENSE00003471480	3384459	3384941
ENSE00003558399	3390423	3390517
ENSE00003621036	3390010	3390133
ENSE00003631106	3393649	3393814

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 88.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0320 / max 43.0608, expressed in 1711 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156030	5.0320	1711

Top tissues by expression

282 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	88.29	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.96	gold quality
right uterine tube	UBERON:0001302	86.57	gold quality
granulocyte	CL:0000094	84.33	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.99	gold quality
adenohypophysis	UBERON:0002196	83.85	gold quality
left ovary	UBERON:0002119	83.30	gold quality
cortical plate	UBERON:0005343	83.14	gold quality
pituitary gland	UBERON:0000007	82.13	gold quality
right ovary	UBERON:0002118	82.06	gold quality
spinal cord	UBERON:0002240	81.66	gold quality
ventricular zone	UBERON:0003053	81.54	gold quality
islet of Langerhans	UBERON:0000006	81.52	gold quality
ganglionic eminence	UBERON:0004023	81.37	gold quality
descending thoracic aorta	UBERON:0002345	81.25	gold quality
apex of heart	UBERON:0002098	81.20	gold quality
diaphragm	UBERON:0001103	81.13	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.08	gold quality
cerebellar hemisphere	UBERON:0002245	81.03	gold quality
mucosa of stomach	UBERON:0001199	80.97	gold quality
cerebellar cortex	UBERON:0002129	80.95	gold quality
blood	UBERON:0000178	80.84	gold quality
lower esophagus muscularis layer	UBERON:0035833	80.77	gold quality
right lobe of thyroid gland	UBERON:0001119	80.75	gold quality
lower esophagus	UBERON:0013473	80.75	gold quality
stromal cell of endometrium	CL:0002255	80.69	gold quality
ovary	UBERON:0000992	80.68	gold quality
right adrenal gland cortex	UBERON:0035827	80.56	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	80.56	gold quality
left adrenal gland	UBERON:0001234	80.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting ZSCAN32, 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-126-5P	100.00	72.71	3180
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-367-5P	98.84	67.18	902
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-619-3P	98.38	65.58	693
HSA-MIR-4684-3P	98.24	69.91	1075
HSA-MIR-1255B-2-3P	97.80	67.04	880
HSA-MIR-490-3P	97.79	65.54	606

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	hb	FBGN0001180
drosophila_melanogaster	CG12391	FBGN0033581
caenorhabditis_elegans		WBGENE00001824
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), ZSCAN1 (ENSG00000152467), 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 32 — Q9NX65 (reviewed: Q9NX65)

Alternative names: Human cervical cancer suppressor gene 5 protein, Zinc finger protein 434

All UniProt accessions (8): Q9NX65, B4DR24, I3L1K0, I3L1S7, I3L2L7, I3L2V3, I3L3Y8, I3L4W6

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 (3)

UniProt ID	Names	Canonical?
Q9NX65-1	1	yes
Q9NX65-2	2
Q9NX65-3	3

RefSeq proteins (11): NP_001271456, NP_001271457, NP_001271458, NP_001311269, NP_001311270, NP_001311271, NP_001311272, NP_001311273, NP_001311274, NP_001311275, NP_060280 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily
IPR044822	Myb_DNA-bind_4	Domain
IPR050688	Zinc_finger/UBP_domain	Family

Pfam: PF00096, PF02023, PF13837

UniProt features (25 total): zinc finger region 6, region of interest 4, compositionally biased region 4, cross-link 4, domain 2, splice variant 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NX65-F1	54.61	0.00

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 (4): 152, 163, 400, 685

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 66 (showing top): CCCNNNNNNAAGWT_UNKNOWN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, AACTTT_UNKNOWN, ACEVEDO_LIVER_CANCER_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HUTTMANN_B_CLL_POOR_SURVIVAL_UP, MARTENS_TRETINOIN_RESPONSE_DN, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, FIGUEROA_AML_METHYLATION_CLUSTER_7_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, PRKDC_TARGET_GENES, RBM34_TARGET_GENES, SRSF9_TARGET_GENES, ZNF711_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 (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), identical protein binding (GO:0042802), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

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
protein binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

974 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN32	C1orf167	Q5SNV9	471
ZSCAN32	MAD1L1	Q9Y6D9	471
ZSCAN32	USP15	Q9Y4E8	439
ZSCAN32	NAA60	Q9H7X0	400
ZSCAN32	TMEM151A	Q8N4L1	393
ZSCAN32	TMEM147	Q9BVK8	363
ZSCAN32	TM4SF20	Q53R12	360
ZSCAN32	PXDC1	Q5TGL8	348
ZSCAN32	KNDC1	Q76NI1	335
ZSCAN32	MIDEAS	Q6PJG2	325
ZSCAN32	SLC22A23	A1A5C7	307
ZSCAN32	ARL17B	I3L3L1	305
ZSCAN32	DEFB129	Q9H1M3	304
ZSCAN32	CRISPLD1	Q9H336	300
ZSCAN32	ARL17A	Q8IVW1	300

IntAct

60 interactions, top by confidence:

A	B	Type	Score
ZNF24	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.880
ZSCAN32	ZNF24	psi-mi:“MI:0915”(physical association)	0.880
ZSCAN32	ZNF24	psi-mi:“MI:0914”(association)	0.880
ZSCAN22	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.800
ZSCAN32	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.800
ZKSCAN1	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.800
ZKSCAN4	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.800
ZSCAN32	ZKSCAN1	psi-mi:“MI:0915”(physical association)	0.800
ZSCAN32	ZKSCAN4	psi-mi:“MI:0915”(physical association)	0.800
SCAND1	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.750
ZSCAN32	SCAND1	psi-mi:“MI:0915”(physical association)	0.750
ZNF446	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN32	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN32	ZNF446	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (130): ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZSCAN32 (Two-hybrid), ZNF446 (Two-hybrid), ZNF396 (Two-hybrid), ZSCAN22 (Two-hybrid), ZKSCAN4 (Two-hybrid), ZSCAN32 (Affinity Capture-RNA), ZSCAN32 (Affinity Capture-RNA), HSPA8 (Affinity Capture-MS), UBR3 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A6NDS4, A6NER0, A6QPT6, B9A6J9, M3WHG5, O14771, O15482, O15553, O19110, O76081, P0C7X1, P0C7X3, P0C7X4, P35125, P48778, P48967, P79209, Q13670, Q15697, Q2TBC4, Q3T191, Q3UZD7, Q4R2Z8, Q5DRQ5, Q5SSQ6, Q5XFX8, Q69ZB3, Q6DHY5, Q6IPX1, Q6ZMN8, Q8BLR5, Q8BWA8, Q8IYF1, Q8IZP1, Q8JZW5, Q8N7G0

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1622 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3384495:T:A	donor_gain	1.0000
16:3384503:T:TA	donor_gain	1.0000
16:3384750:A:C	donor_gain	1.0000
16:3400943:A:AC	donor_gain	1.0000
16:3400944:C:CC	donor_gain	1.0000
16:3384452:GTCTT:G	donor_loss	0.9900
16:3384453:TCTTA:T	donor_loss	0.9900
16:3384454:CTTA:C	donor_loss	0.9900
16:3384455:TTA:T	donor_loss	0.9900
16:3384456:TACCA:T	donor_loss	0.9900
16:3384457:ACCA:A	donor_loss	0.9900
16:3384458:C:T	donor_loss	0.9900
16:3384942:C:CC	acceptor_gain	0.9900
16:3390513:CCAGG:C	acceptor_gain	0.9900
16:3390514:CAGGC:C	acceptor_gain	0.9900
16:3395486:T:A	acceptor_gain	0.9900
16:3397180:T:TA	donor_gain	0.9900
16:3400939:ACT:A	donor_loss	0.9900
16:3400940:CTCA:C	donor_loss	0.9900
16:3400941:TCA:T	donor_loss	0.9900
16:3400942:CACCG:C	donor_loss	0.9900
16:3400944:C:CA	donor_loss	0.9900
16:3400944:CCGGA:C	donor_gain	0.9900
16:3400975:C:CA	donor_gain	0.9900
16:3384939:TTG:T	acceptor_gain	0.9800
16:3390514:CAGG:C	acceptor_gain	0.9800
16:3390518:C:CC	acceptor_gain	0.9800
16:3397186:TCTCA:T	donor_loss	0.9800
16:3397187:CTCA:C	donor_loss	0.9800
16:3397188:TCA:T	donor_loss	0.9800

AlphaMissense

4619 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3383272:A:C	F558L	0.999
16:3383272:A:T	F558L	0.999
16:3383274:A:G	F558L	0.999
16:3382936:G:C	F670L	0.998
16:3382936:G:T	F670L	0.998
16:3382938:A:G	F670L	0.998
16:3383104:G:C	F614L	0.998
16:3383104:G:T	F614L	0.998
16:3383106:A:G	F614L	0.998
16:3383188:G:C	F586L	0.998
16:3383188:G:T	F586L	0.998
16:3383190:A:G	F586L	0.998
16:3383356:A:C	F530L	0.997
16:3383356:A:T	F530L	0.997
16:3383358:A:G	F530L	0.997
16:3382937:A:G	F670S	0.996
16:3383118:A:G	C610R	0.996
16:3383273:A:G	F558S	0.996
16:3383020:G:C	F642L	0.995
16:3383020:G:T	F642L	0.995
16:3383022:A:G	F642L	0.995
16:3383043:A:G	C635R	0.995
16:3383072:C:G	R625P	0.995
16:3383105:A:G	F614S	0.995
16:3383127:A:G	C607R	0.995
16:3383163:G:C	H595D	0.995
16:3383189:A:G	F586S	0.995
16:3383240:C:G	R569P	0.995
16:3383255:A:G	L564P	0.995
16:3383331:G:C	H539D	0.995

dbSNP variants (sampled 300 via entrez): RS1000137071 (16:3386892 GTAAC>G), RS1000142330 (16:3390418 C>T), RS1000252579 (16:3390655 C>A,G), RS1000553807 (16:3400130 A>G,T), RS1000688036 (16:3400359 C>A), RS1000860821 (16:3393588 T>C), RS1000918311 (16:3389781 G>A), RS1001462636 (16:3395374 G>C), RS1001494711 (16:3399634 T>C), RS1001577316 (16:3395669 G>A), RS1001707959 (16:3388729 A>T), RS1001736835 (16:3389956 T>A,C), RS1001760522 (16:3388381 C>G,T), RS1001848094 (16:3400903 C>T), RS1002013456 (16:3395891 G>T)

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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, decreases expression	2
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
beta-lapachone	increases expression	1
benzo(e)pyrene	increases methylation	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
Temozolomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Ozone	affects expression, increases abundance	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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