ZKSCAN7

Summary

ZKSCAN7 (zinc finger with KRAB and SCAN domains 7, HGNC:12955) is a protein-coding gene on chromosome 3p21.31, encoding Zinc finger protein with KRAB and SCAN domains 7 (Q9P0L1). 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 active in nucleus.

Source: NCBI Gene 55888 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 106 total
• Transcription factor: yes — 14 downstream targets (CollecTRI)
• MANE Select transcript: NM_001288590

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12955
Approved symbol	ZKSCAN7
Name	zinc finger with KRAB and SCAN domains 7
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12738, ZSCAN39
Ensembl gene	ENSG00000196345
Ensembl biotype	protein_coding
Entrez	55888

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 15 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000273320, ENST00000341840, ENST00000418719, ENST00000419137, ENST00000426540, ENST00000431636, ENST00000447279, ENST00000496563, ENST00000896017, ENST00000896018, ENST00000896019, ENST00000932839, ENST00000946797, ENST00000946798, ENST00000946799, ENST00000946800, ENST00000946801

RefSeq mRNA: 5 — MANE Select: NM_001288590 NM_001288590, NM_001288591, NM_001288592, NM_018651, NM_025169

CCDS: CCDS2714, CCDS2715, CCDS74924

Canonical transcript exons

ENST00000426540 — 6 exons

Exon	Start	End
ENSE00000967144	44569922	44572158
ENSE00001236042	44556930	44557470
ENSE00001657475	44555193	44555481
ENSE00003524420	44565487	44565655
ENSE00003780619	44567912	44568003
ENSE00003781396	44568307	44568433

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 81.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3491 / max 79.6010, expressed in 1272 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36332	5.3491	1272

Top tissues by expression

137 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	81.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.69	gold quality
ganglionic eminence	UBERON:0004023	80.44	gold quality
cortical plate	UBERON:0005343	79.77	gold quality
ventricular zone	UBERON:0003053	75.61	gold quality
islet of Langerhans	UBERON:0000006	75.13	gold quality
endometrium	UBERON:0001295	74.24	gold quality
right ovary	UBERON:0002118	73.89	gold quality
ovary	UBERON:0000992	73.72	gold quality
left ovary	UBERON:0002119	73.67	gold quality
smooth muscle tissue	UBERON:0001135	73.53	gold quality
adrenal tissue	UBERON:0018303	73.22	gold quality
pancreas	UBERON:0001264	72.33	gold quality
pituitary gland	UBERON:0000007	72.22	gold quality
fallopian tube	UBERON:0003889	72.19	gold quality
right adrenal gland	UBERON:0001233	71.91	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.63	gold quality
right uterine tube	UBERON:0001302	71.62	gold quality
body of uterus	UBERON:0009853	71.57	gold quality
cerebellar hemisphere	UBERON:0002245	71.56	gold quality
cerebellum	UBERON:0002037	71.54	gold quality
cerebellar cortex	UBERON:0002129	71.54	gold quality
adrenal gland	UBERON:0002369	71.53	gold quality
left adrenal gland	UBERON:0001234	71.50	gold quality
stromal cell of endometrium	CL:0002255	71.48	gold quality
left adrenal gland cortex	UBERON:0035825	71.40	gold quality
lymph node	UBERON:0000029	71.38	gold quality
apex of heart	UBERON:0002098	71.35	gold quality
body of pancreas	UBERON:0001150	71.27	gold quality
adenohypophysis	UBERON:0002196	70.76	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.58

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

14 targets.

Target	Regulation
AP3B1
CBX1
CHEK2
EPCAM
FGFR1
GDNF
IGF2
INS
KRT9
ME3
POU5F1	Activation
PTCH1
TERT
TRIM28

Upstream regulators (CollecTRI, top): PGR

miRNA regulators (miRDB)

79 targeting ZKSCAN7, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zkscan7	ENSMUSG00000063488
rattus_norvegicus	Zkscan7	ENSRNOG00000004104

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein with KRAB and SCAN domains 7 — Q9P0L1 (reviewed: Q9P0L1)

Alternative names: Zinc finger protein 167, Zinc finger protein 448, Zinc finger protein 64

All UniProt accessions (4): C9J6L6, Q9P0L1, E7EMM9, H7BZE7

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?
Q9P0L1-1	1	yes
Q9P0L1-2	2

RefSeq proteins (5): NP_001275519, NP_001275520, NP_001275521, NP_061121, NP_079445 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
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

Pfam: PF00096, PF01352, PF02023

UniProt features (31 total): zinc finger region 13, sequence variant 7, domain 2, region of interest 2, compositionally biased region 2, splice variant 2, chain 1, cross-link 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P0L1-F1	66.29	0.05

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): 28

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 78 (showing top): MODULE_255, MODULE_45, MODULE_317, MODULE_157, MODULE_113, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MODULE_60, MODULE_38, MODULE_69, SCGGAAGY_ELK1_02, MODULE_13, POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP, MODULE_23, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_41

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), 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)

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
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

568 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZKSCAN7	TRIM28	Q13263	944
ZKSCAN7	SETDB1	Q15047	893
ZKSCAN7	CBX5	P45973	592
ZKSCAN7	TRPS1	Q9UHF7	555
ZKSCAN7	ZPR1	O75312	521
ZKSCAN7	RUNX3	Q13761	508
ZKSCAN7	EBF1	Q9UH73	450
ZKSCAN7	MMP13	P45452	423
ZKSCAN7	IHH	Q14623	403
ZKSCAN7	SPP1	P10451	388
ZKSCAN7	YIPF2	Q9BWQ6	370
ZKSCAN7	EHMT2	Q96KQ7	370
ZKSCAN7	DOCK5	Q9H7D0	370
ZKSCAN7	RUNX2	Q13950	361
ZKSCAN7	DNMT3A	Q9Y6K1	349

IntAct

23 interactions, top by confidence:

A	B	Type	Score
SCAND1	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.670
ZKSCAN7	ZKSCAN4	psi-mi:“MI:0915”(physical association)	0.670
ZKSCAN7	SCAND1	psi-mi:“MI:0915”(physical association)	0.670
ZKSCAN4	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.670
ZKSCAN7	ZSCAN12	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN7	ZNF446	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN7	ZSCAN21	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN21	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN7	TIMM50	psi-mi:“MI:0915”(physical association)	0.400
NFIC	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.370
ZSCAN32	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.370
C9orf72	CHD2	psi-mi:“MI:0914”(association)	0.350
CBX2	TRANK1	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN4 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), TCEANC (Two-hybrid), ZKSCAN7 (Two-hybrid), ZKSCAN7 (Two-hybrid), ZSCAN12 (Two-hybrid), ZKSCAN7 (Reconstituted Complex), ZKSCAN7 (Two-hybrid), ZKSCAN7 (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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	91
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1523 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44557468:G:GT	donor_gain	1.0000
3:44568967:A:AG	acceptor_gain	1.0000
3:44568967:ACTT:A	acceptor_gain	1.0000
3:44586103:A:AG	acceptor_gain	1.0000
3:44586104:G:GG	acceptor_gain	1.0000
3:44557467:GGAG:G	donor_gain	0.9900
3:44557468:GAGG:G	donor_loss	0.9900
3:44557469:AGGT:A	donor_loss	0.9900
3:44557470:GGTGA:G	donor_loss	0.9900
3:44557471:G:GA	donor_loss	0.9900
3:44557479:T:G	donor_gain	0.9900
3:44565677:GCCT:G	donor_gain	0.9900
3:44568968:C:G	acceptor_gain	0.9900
3:44569915:T:TA	acceptor_gain	0.9900
3:44569916:G:A	acceptor_gain	0.9900
3:44586103:AGT:A	acceptor_gain	0.9900
3:44586104:GT:G	acceptor_gain	0.9900
3:44586104:GTG:G	acceptor_gain	0.9900
3:44586212:GG:G	donor_gain	0.9900
3:44586213:GG:G	donor_gain	0.9900
3:44587236:G:GT	donor_gain	0.9900
3:44587251:G:GG	donor_gain	0.9900
3:44556928:A:AG	acceptor_gain	0.9800
3:44556929:G:GG	acceptor_gain	0.9800
3:44557468:GAG:G	donor_gain	0.9800
3:44565553:G:GT	donor_gain	0.9800
3:44567910:A:AG	acceptor_gain	0.9800
3:44567911:G:GG	acceptor_gain	0.9800
3:44567911:GCTCA:G	acceptor_gain	0.9800
3:44568966:C:G	acceptor_gain	0.9800

AlphaMissense

5003 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44571040:T:C	F644L	0.999
3:44571042:C:A	F644L	0.999
3:44571042:C:G	F644L	0.999
3:44571208:T:C	F700L	0.999
3:44571210:T:A	F700L	0.999
3:44571210:T:G	F700L	0.999
3:44571059:T:C	L650P	0.998
3:44571067:C:G	H653D	0.998
3:44571124:T:C	F672L	0.998
3:44571126:C:A	F672L	0.998
3:44571126:C:G	F672L	0.998
3:44571151:C:G	H681D	0.998
3:44571227:T:C	L706P	0.998
3:44571292:T:C	F728L	0.998
3:44571294:T:A	F728L	0.998
3:44571294:T:G	F728L	0.998
3:44571071:A:C	Q654P	0.997
3:44571235:C:G	H709D	0.997
3:44571239:A:C	Q710P	0.997
3:44570956:T:C	F616L	0.996
3:44570958:T:A	F616L	0.996
3:44570958:T:G	F616L	0.996
3:44571069:C:A	H653Q	0.996
3:44571069:C:G	H653Q	0.996
3:44571143:T:C	L678P	0.996
3:44571153:T:A	H681Q	0.996
3:44571153:T:G	H681Q	0.996
3:44570368:T:C	F420L	0.995
3:44570370:C:A	F420L	0.995
3:44570370:C:G	F420L	0.995

dbSNP variants (sampled 300 via entrez): RS1000291492 (3:44564793 T>G), RS1000373011 (3:44579639 T>C), RS1000420526 (3:44579435 G>A), RS1000530575 (3:44568814 A>G), RS1000595562 (3:44575001 T>C,G), RS1000645623 (3:44578228 T>C), RS1000700183 (3:44561810 G>A,C), RS1000938105 (3:44553409 G>T), RS1000938316 (3:44581745 C>G), RS1001130614 (3:44561584 A>G), RS1001217522 (3:44569113 G>A), RS1001256381 (3:44555557 G>C), RS1001285248 (3:44557507 C>T), RS1001550952 (3:44573574 A>G), RS1001694194 (3:44560495 G>C,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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
testosterone undecanoate	affects cotreatment, increases expression	1
arsenite	increases methylation	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
clothianidin	increases expression	1
eprenetapopt	affects expression, affects reaction	1
Sunitinib	decreases expression	1
Arbutin	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Benztropine	decreases expression	1
Caffeine	increases phosphorylation	1
Calcitriol	increases expression	1
Cannabidiol	decreases expression	1
Formaldehyde	decreases expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Silicon Dioxide	decreases expression	1
Dronabinol	decreases expression, decreases response to substance	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Levonorgestrel	affects cotreatment, increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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