ZSCAN12

Summary

ZSCAN12 (zinc finger and SCAN domain containing 12, HGNC:13172) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger and SCAN domain-containing protein 12 (O43309). 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 9753 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_001163391

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13172
Approved symbol	ZSCAN12
Name	zinc finger and SCAN domain containing 12
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2
Ensembl gene	ENSG00000158691
Ensembl biotype	protein_coding
OMIM	603978
Entrez	9753

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000361028, ENST00000396827, ENST00000684592, ENST00000947375

RefSeq mRNA: 2 — MANE Select: NM_001163391 NM_001163391, NM_001368124

CCDS: CCDS93876

Canonical transcript exons

ENST00000684592 — 4 exons

Exon	Start	End
ENSE00000848557	28392902	28393046
ENSE00001175574	28398004	28398473
ENSE00003919488	28399657	28399747
ENSE00003922307	28384738	28391742

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 82.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3960 / max 58.5584, expressed in 1325 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72416	2.3683	1163
72415	0.6877	409
72417	0.2149	90
72414	0.1251	45

Top tissues by expression

273 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	82.82	gold quality
ventricular zone	UBERON:0003053	81.89	gold quality
ganglionic eminence	UBERON:0004023	80.67	gold quality
cortical plate	UBERON:0005343	79.51	gold quality
embryo	UBERON:0000922	78.20	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.73	gold quality
endothelial cell	CL:0000115	77.08	silver quality
sperm	CL:0000019	76.22	silver quality
choroid plexus epithelium	UBERON:0003911	75.81	silver quality
endometrium epithelium	UBERON:0004811	75.48	silver quality
hair follicle	UBERON:0002073	75.42	silver quality
pancreatic ductal cell	CL:0002079	74.71	gold quality
calcaneal tendon	UBERON:0003701	74.36	gold quality
male germ cell	CL:0000015	74.08	silver quality
islet of Langerhans	UBERON:0000006	74.03	gold quality
adrenal tissue	UBERON:0018303	74.00	gold quality
stromal cell of endometrium	CL:0002255	73.87	gold quality
germinal epithelium of ovary	UBERON:0001304	72.95	gold quality
ovary	UBERON:0000992	71.89	gold quality
ectocervix	UBERON:0012249	71.31	gold quality
lymph node	UBERON:0000029	71.17	gold quality
pigmented layer of retina	UBERON:0001782	70.93	silver quality
paraflocculus	UBERON:0005351	70.91	gold quality
left ovary	UBERON:0002119	70.90	gold quality
body of uterus	UBERON:0009853	70.89	gold quality
rectum	UBERON:0001052	70.72	gold quality
pancreas	UBERON:0001264	70.58	gold quality
right ovary	UBERON:0002118	70.54	gold quality
muscle layer of sigmoid colon	UBERON:0035805	70.54	gold quality
middle frontal gyrus	UBERON:0002702	70.42	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ENAD-17	no	231.62
E-ANND-3	no	4.84

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Methylation statuses of NCOR2, PARK2, and ZSCAN12 signify densities of tumor-infiltrating lymphocytes in gastric carcinoma. (PMID:35039565)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zscan12	ENSMUSG00000036721
rattus_norvegicus	Zscan12	ENSRNOG00000052959

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), 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 12 — O43309 (reviewed: O43309)

Alternative names: Zinc finger protein 305, Zinc finger protein 96

All UniProt accessions (2): A0A804HJ42, O43309

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?
O43309-1	1	yes
O43309-2	2

RefSeq proteins (2): NP_001156863, NP_001355053 (=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF02023

UniProt features (22 total): zinc finger region 12, cross-link 3, region of interest 2, chain 1, domain 1, compositionally biased region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43309-F1	70.20	0.23

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 (3): 20, 25, 196

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, BROWNE_HCMV_INFECTION_48HR_DN, SCHLOSSER_SERUM_RESPONSE_DN, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, SCGGAAGY_ELK1_02, BOCHKIS_FOXA2_TARGETS, MODULE_13, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, YAGI_AML_WITH_T_8_21_TRANSLOCATION, IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP, MODULE_41

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

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN12	STPG3	Q8N7X2	529
ZSCAN12	SYCP2L	Q5T4T6	417
ZSCAN12	SACK1A	Q86UY5	400
ZSCAN12	NKAPL	Q5M9Q1	397
ZSCAN12	COMMD5	Q9GZQ3	392
ZSCAN12	C1QTNF6	Q9BXI9	389
ZSCAN12	RPS7	P23821	363
ZSCAN12	OR1C1	Q15619	358
ZSCAN12	ARHGAP4	P98171	323
ZSCAN12	SZRD1	Q7Z422	322
ZSCAN12	YIPF6	Q96EC8	307
ZSCAN12	SOWAHC	Q53LP3	304
ZSCAN12	PGBD1	Q96JS3	300
ZSCAN12	TMEM161B	Q8NDZ6	285
ZSCAN12	GPANK1	O95872	276

IntAct

104 interactions, top by confidence:

A	B	Type	Score
ZSCAN12	MID2	psi-mi:“MI:0915”(physical association)	0.720
MID2	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.720
TFIP11	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN12	TFIP11	psi-mi:“MI:0915”(physical association)	0.670
ZSCAN12	ZNF446	psi-mi:“MI:0915”(physical association)	0.600
ZNF446	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.600
ZSCAN12	ZSCAN32	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN32	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN12	CEP70	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN12	ZNF473	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN12	ZNF496	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN7	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
SSX2IP	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
CEP70	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
ZNF496	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN12	SSX2IP	psi-mi:“MI:0915”(physical association)	0.560

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1064 predictions. Top by Δscore:

Variant	Effect	Δscore
6:28392897:TTTA:T	donor_loss	1.0000
6:28392900:A:AT	donor_loss	1.0000
6:28392901:CCTTG:C	donor_gain	1.0000
6:28391743:C:CC	acceptor_gain	0.9900
6:28393046:CCTGA:C	acceptor_loss	0.9900
6:28393047:C:A	acceptor_loss	0.9900
6:28393048:T:A	acceptor_loss	0.9900
6:28397998:TCTCA:T	donor_loss	0.9900
6:28397999:CTCA:C	donor_loss	0.9900
6:28398000:TCA:T	donor_loss	0.9900
6:28398001:CACC:C	donor_loss	0.9900
6:28398002:A:AG	donor_loss	0.9900
6:28398003:C:T	donor_loss	0.9900
6:28398003:CCTG:C	donor_gain	0.9900
6:28390623:T:C	donor_gain	0.9800
6:28391741:AAC:A	acceptor_loss	0.9800
6:28398469:CAGTC:C	acceptor_gain	0.9800
6:28383413:TTC:T	donor_gain	0.9700
6:28398471:GTCCT:G	acceptor_gain	0.9700
6:28399652:CTCA:C	donor_loss	0.9700
6:28399653:TCA:T	donor_loss	0.9700
6:28399654:CAC:C	donor_loss	0.9700
6:28399655:ACCT:A	donor_loss	0.9700
6:28399656:C:A	donor_loss	0.9700
6:28399685:C:CA	donor_gain	0.9700
6:28391741:AA:A	acceptor_gain	0.9600
6:28392900:A:AC	donor_gain	0.9600
6:28392901:C:CC	donor_gain	0.9600
6:28392938:A:AC	donor_gain	0.9600
6:28392939:C:CC	donor_gain	0.9600

AlphaMissense

4070 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:28390772:A:C	F506L	0.999
6:28390772:A:T	F506L	0.999
6:28390774:A:G	F506L	0.999
6:28391105:A:C	F395L	0.999
6:28391105:A:T	F395L	0.999
6:28391107:A:G	F395L	0.999
6:28390688:G:C	F534L	0.998
6:28390688:G:T	F534L	0.998
6:28390690:A:G	F534L	0.998
6:28390824:C:G	R489P	0.998
6:28390755:A:G	L512P	0.997
6:28391021:A:C	F423L	0.997
6:28391021:A:T	F423L	0.997
6:28391023:A:G	F423L	0.997
6:28391189:A:C	F367L	0.997
6:28391189:A:T	F367L	0.997
6:28391191:A:G	F367L	0.997
6:28391273:A:C	F339L	0.997
6:28391273:A:T	F339L	0.997
6:28391275:A:G	F339L	0.997
6:28391357:G:C	F311L	0.997
6:28391357:G:T	F311L	0.997
6:28391359:A:G	F311L	0.997
6:28390743:T:G	Q516P	0.996
6:28390773:A:G	F506S	0.996
6:28390856:A:C	F478L	0.996
6:28390856:A:T	F478L	0.996
6:28390858:A:G	F478L	0.996
6:28390745:A:C	H515Q	0.995
6:28390745:A:T	H515Q	0.995

dbSNP variants (sampled 300 via entrez): RS1000158810 (6:28390933 G>C,T), RS1000448916 (6:28382572 G>A), RS1000607880 (6:28399736 C>G), RS1000610328 (6:28391421 A>G), RS1000725769 (6:28383819 TAGG>T), RS1000728356 (6:28384444 A>G), RS1000782063 (6:28384022 T>C), RS1001104261 (6:28398616 C>T), RS1001488992 (6:28397935 G>T), RS1001663984 (6:28399499 C>T), RS1002001160 (6:28401072 A>G), RS1002055026 (6:28400657 C>G), RS1002221049 (6:28384761 T>C), RS1002226360 (6:28393696 C>A), RS1002399371 (6:28386195 C>T)

Disease associations

OMIM: gene MIM:603978 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

23 associations (top):

Study	Trait	p-value
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_212	Autism spectrum disorder or schizophrenia	5.000000e-14
GCST004521_43	Autism spectrum disorder or schizophrenia	2.000000e-27
GCST004521_7	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004521_77	Autism spectrum disorder or schizophrenia	1.000000e-19
GCST004748_10	Lung cancer	7.000000e-12
GCST004750_41	Squamous cell lung carcinoma	7.000000e-11
GCST005541_3	Sarcoidosis (Lofgren’s syndrome vs non-Lofgren’s syndrome)	5.000000e-18
GCST007559_16	Sleep duration (short sleep)	4.000000e-09
GCST008810_77	Smoking initiation (ever regular vs never regular)	1.000000e-08
GCST008921_4	Asthma and major depressive disorder	2.000000e-11
GCST010002_50	Refractive error	4.000000e-34
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST011766_13	Chronic obstructive pulmonary disease	2.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005670	smoking initiation
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	3
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
trichostatin A	affects cotreatment, affects methylation, decreases reaction	1
sodium arsenite	affects cotreatment, affects methylation, decreases reaction, affects acetylation, decreases expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
monomethylarsonous acid	affects acetylation, affects methylation, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
abrine	increases expression	1
dorsomorphin	increases expression, affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	decreases reaction, affects cotreatment, affects methylation	1
Vorinostat	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methotrexate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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