ZKSCAN5

gene
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Also known as ZNF914ZSCAN37

Summary

ZKSCAN5 (zinc finger with KRAB and SCAN domains 5, HGNC:12867) is a protein-coding gene on chromosome 7q22.1, encoding Zinc finger protein with KRAB and SCAN domains 5 (Q9Y2L8). May be involved in transcriptional regulation.

This gene encodes a zinc finger protein of the Kruppel family. The protein contains a SCAN box and a KRAB A domain and may be involved in transcriptional regulation. A similar protein in mouse is differentially expressed in spermatogenesis. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 23660 — RefSeq curated summary.

At a glance

  • GWAS associations: 18
  • Clinical variants (ClinVar): 100 total
  • MANE Select transcript: NM_145102

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12867
Approved symbolZKSCAN5
Namezinc finger with KRAB and SCAN domains 5
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesZNF914, ZSCAN37
Ensembl geneENSG00000196652
Ensembl biotypeprotein_coding
OMIM611272
Entrez23660

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 19 protein_coding, 1 nonsense_mediated_decay

ENST00000326775, ENST00000394170, ENST00000451158, ENST00000454175, ENST00000864572, ENST00000864573, ENST00000864574, ENST00000864575, ENST00000864576, ENST00000864577, ENST00000925936, ENST00000925937, ENST00000925938, ENST00000925939, ENST00000925940, ENST00000925941, ENST00000925942, ENST00000925943, ENST00000970506, ENST00000970507

RefSeq mRNA: 5 — MANE Select: NM_145102 NM_001318082, NM_001318083, NM_001318084, NM_014569, NM_145102

CCDS: CCDS5667

Canonical transcript exons

ENST00000326775 — 7 exons

ExonStartEnd
ENSE000007082669951982799519909
ENSE000011029729952016999520304
ENSE000012890809950466299504733
ENSE000013750219950600599506458
ENSE000013853269951245399512591
ENSE000018663989953110899534700
ENSE000034962049952581399526418

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 88.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.8459 / max 78.0778, expressed in 1772 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
798834.64781664
798811.60681026
798821.5913970

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818888.00gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.03gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.64gold quality
ventricular zoneUBERON:000305383.47gold quality
ganglionic eminenceUBERON:000402382.70gold quality
cortical plateUBERON:000534382.25gold quality
spermCL:000001982.05gold quality
stromal cell of endometriumCL:000225580.06gold quality
male germ cellCL:000001579.37gold quality
tendonUBERON:000004378.82gold quality
hindlimb stylopod muscleUBERON:000425277.91gold quality
adrenal tissueUBERON:001830377.76gold quality
islet of LangerhansUBERON:000000677.61gold quality
gastrocnemiusUBERON:000138877.50gold quality
muscle of legUBERON:000138377.46gold quality
calcaneal tendonUBERON:000370176.74gold quality
granulocyteCL:000009476.48gold quality
cerebellar hemisphereUBERON:000224576.44gold quality
endothelial cellCL:000011576.42silver quality
cerebellar cortexUBERON:000212976.41gold quality
embryoUBERON:000092276.09gold quality
right hemisphere of cerebellumUBERON:001489075.58gold quality
prefrontal cortexUBERON:000045175.34gold quality
right adrenal gland cortexUBERON:003582775.15gold quality
cerebellumUBERON:000203775.12gold quality
right adrenal glandUBERON:000123375.04gold quality
leukocyteCL:000073874.88gold quality
testisUBERON:000047374.65gold quality
monocyteCL:000057674.52gold quality
secondary oocyteCL:000065574.51gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.30

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1652.1ZKSCAN5Factors with multiple dispersed zinc fingers
MA1652.2ZKSCAN5Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:23354101

miRNA regulators (miRDB)

63 targeting ZKSCAN5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-223-3P99.9970.141140
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-211099.9666.681930
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-345-3P99.8970.231421
HSA-MIR-430299.8967.941187
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-605-3P99.8869.221833
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-431999.7669.832586
HSA-MIR-187-5P99.7470.261404
HSA-MIR-3913-3P99.7466.53938
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-128399.6972.423009
HSA-MIR-670-5P99.6769.941565

Literature-anchored findings (GeneRIF, showing 2)

  • Shorter telomeres increase chronic obstructive pulmonary disease (COPD) risk and the zinc finger protein 95 homolog ZFP95 (ZNF208) polymorphism affects telomere length in COPD patients. (PMID:30397981)
  • ZKSCAN5 activates LAPTM5 expression by recruiting SETD7 to promote metastasis in pancreatic ductal adenocarcinoma. (PMID:38018874)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZkscan5ENSMUSG00000055991
rattus_norvegicusZkscan5ENSRNOG00000059552

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein with KRAB and SCAN domains 5Q9Y2L8 (reviewed: Q9Y2L8)

Alternative names: Zinc finger protein 95 homolog

All UniProt accessions (2): Q9Y2L8, F8WBD4

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 (5): NP_001305011, NP_001305012, NP_001305013, NP_055384, NP_659570* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF01352, PF02023

UniProt features (57 total): strand 17, zinc finger region 13, helix 10, cross-link 9, turn 4, domain 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
2EM5SOLUTION NMR
2EMMSOLUTION NMR
2EMZSOLUTION NMR
2EN3SOLUTION NMR
2EOMSOLUTION NMR
2EONSOLUTION NMR
2EOOSOLUTION NMR
2YSOSOLUTION NMR
2YTGSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2L8-F158.550.04

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 (10): 335, 216, 248, 270, 303, 317, 509, 513, 709, 785

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 131 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GSE45365_NK_CELL_VS_CD8_TCELL_UP, TTTGTAG_MIR520D, HFH8_01, TGACATY_UNKNOWN, BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP, LEE_AGING_NEOCORTEX_DN, MODULE_207, DANG_BOUND_BY_MYC, CETS1P54_01, PARENT_MTOR_SIGNALING_UP, BENPORATH_OCT4_TARGETS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, BENPORATH_MYC_MAX_TARGETS, SCGGAAGY_ELK1_02

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of macromolecule biosynthetic process (GO:0010558)

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), DNA-binding transcription factor activity (GO:0003700), 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)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription by RNA polymerase II1
macromolecule biosynthetic process1
negative regulation of biosynthetic process1
regulation of macromolecule biosynthetic process1
negative regulation of macromolecule metabolic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transcription cis-regulatory region binding1
transcription regulator activity1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1042 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZKSCAN5CNOT10Q9H9A5623
ZKSCAN5FCF1Q9Y324559
ZKSCAN5AMMECR1LQ6DCA0542
ZKSCAN5USP39Q53GS9539
ZKSCAN5TLK2Q86UE8499
ZKSCAN5ARPC1AQ92747492
ZKSCAN5DHX16O60231490
ZKSCAN5NPIPB6E9PJ23480
ZKSCAN5DDX50Q9BQ39473
ZKSCAN5NOL7Q9UMY1465
ZKSCAN5TMUB2Q71RG4463
ZKSCAN5SLC4A1APQ9BWU0460
ZKSCAN5GPATCH3Q96I76444
ZKSCAN5NUDCD3Q8IVD9429
ZKSCAN5AGKQ53H12420

IntAct

28 interactions, top by confidence:

ABTypeScore
ZKSCAN5GFAPpsi-mi:“MI:0915”(physical association)0.560
ZKSCAN5GLE1psi-mi:“MI:0915”(physical association)0.560
ZKSCAN5ATXN10psi-mi:“MI:0915”(physical association)0.560
ZKSCAN5SPRED1psi-mi:“MI:0915”(physical association)0.560
SUV39H1ZKSCAN5psi-mi:“MI:0915”(physical association)0.510
CRKZKSCAN5psi-mi:“MI:0407”(direct interaction)0.440
CCL1ZKSCAN5psi-mi:“MI:0915”(physical association)0.370
ZKSCAN5ZBTB9psi-mi:“MI:0915”(physical association)0.370
ZKSCAN5ZSCAN1psi-mi:“MI:0915”(physical association)0.370
TNNT1ZKSCAN5psi-mi:“MI:0915”(physical association)0.370
ZSCAN20ZNF197psi-mi:“MI:0914”(association)0.350
ZNF232ZNF197psi-mi:“MI:0914”(association)0.350
ZKSCAN5DNAJB6psi-mi:“MI:0914”(association)0.350
ZSCAN21IPO8psi-mi:“MI:0914”(association)0.350
fadLZKSCAN5psi-mi:“MI:0915”(physical association)0.000
ZKSCAN5psi-mi:“MI:0915”(physical association)0.000
RBM11ZKSCAN5psi-mi:“MI:0915”(physical association)0.000

BioGRID (19): ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-RNA), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Affinity Capture-MS), ZKSCAN5 (Reconstituted Complex), ZKSCAN5 (Protein-peptide), ZKSCAN5 (Two-hybrid), PPA1 (Cross-Linking-MS (XL-MS)), ZBTB9 (Two-hybrid), ZSCAN1 (Two-hybrid), ZKSCAN5 (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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance88
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1328 predictions. Top by Δscore:

VariantEffectΔscore
7:99504731:GAG:Gdonor_gain1.0000
7:99506455:GCAG:Gdonor_gain1.0000
7:99506457:AGGTG:Adonor_loss1.0000
7:99506458:GGTG:Gdonor_loss1.0000
7:99506459:G:Adonor_loss1.0000
7:99506460:T:Adonor_loss1.0000
7:99512443:T:TAacceptor_gain1.0000
7:99512448:GTTA:Gacceptor_loss1.0000
7:99512449:TTA:Tacceptor_loss1.0000
7:99512450:TA:Tacceptor_loss1.0000
7:99512451:A:AGacceptor_gain1.0000
7:99512452:G:GGacceptor_gain1.0000
7:99512452:GATT:Gacceptor_gain1.0000
7:99519825:A:AGacceptor_gain1.0000
7:99519826:G:GGacceptor_gain1.0000
7:99520168:GAA:Gacceptor_gain1.0000
7:99526414:GAGAT:Gdonor_gain1.0000
7:99529654:G:GTdonor_gain1.0000
7:99531107:GGCA:Gacceptor_gain1.0000
7:99504724:T:TAdonor_gain0.9900
7:99504725:G:GAdonor_gain0.9900
7:99504731:GAGGT:Gdonor_loss0.9900
7:99504733:GGT:Gdonor_loss0.9900
7:99504734:G:GAdonor_loss0.9900
7:99504735:T:Gdonor_loss0.9900
7:99505365:A:Tdonor_gain0.9900
7:99506003:A:AGacceptor_gain0.9900
7:99506004:G:GGacceptor_gain0.9900
7:99506004:GT:Gacceptor_gain0.9900
7:99506461:GAG:Gdonor_loss0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000031988 (7:99524869 A>C), RS1000139139 (7:99526988 G>A), RS1000171680 (7:99508258 C>A,T), RS1000350807 (7:99520774 T>G), RS1000424408 (7:99514945 T>G), RS1000500159 (7:99512657 C>T), RS1000544518 (7:99531353 T>G), RS1000552235 (7:99512891 T>C), RS1000561038 (7:99507115 A>G), RS1000582612 (7:99525321 A>G), RS1000648285 (7:99526442 G>A,C,T), RS1000819719 (7:99520040 C>G,T), RS1000828054 (7:99507538 T>C), RS1001142836 (7:99533108 T>G), RS1001230513 (7:99519690 G>T)

Disease associations

OMIM: gene MIM:611272 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

StudyTraitp-value
GCST001038_1Dehydroepiandrosterone sulphate levels3.000000e-36
GCST002925_11Sex hormone levels2.000000e-14
GCST002925_12Sex hormone levels2.000000e-07
GCST002925_6Sex hormone levels6.000000e-14
GCST004730_2Facial emotion recognition (sad faces)3.000000e-06
GCST005144_1Tacrolimus trough concentration in kidney transplant patients2.000000e-17
GCST005348_113Total body bone mineral density1.000000e-08
GCST005795_25Femoral neck bone mineral density8.000000e-06
GCST005796_12Lumbar spine bone mineral density1.000000e-08
GCST005830_30Hand grip strength2.000000e-08
GCST006249_21Serum metabolite levels4.000000e-11
GCST006249_22Serum metabolite levels2.000000e-12
GCST009163_1Hormone measurements2.000000e-08
GCST009163_2Hormone measurements2.000000e-09
GCST009733_105Urinary metabolite levels in chronic kidney disease6.000000e-18
GCST009733_120Urinary metabolite levels in chronic kidney disease2.000000e-12
GCST009733_239Urinary metabolite levels in chronic kidney disease6.000000e-12
GCST90002407_487White blood cell count1.000000e-09

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0004730hormone measurement
EFO:0007001dehydroepiandrosterone sulphate measurement
EFO:0004908testosterone measurement
EFO:0008329facial emotion recognition measurement
EFO:0008458tacrolimus measurement
EFO:0007785femoral neck bone mineral density
EFO:0007701spine bone mineral density
EFO:0006941grip strength measurement
EFO:0010239cortisol:DHEAS ratio measurement
EFO:0010240dehydroepiandrosterone measurement
EFO:0005116urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
trichostatin Aaffects cotreatment, decreases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
FR900359decreases phosphorylation1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
sodium arseniteincreases expression1
perfluorooctanoic aciddecreases expression1
4-nitroso-N-phenylanilineaffects response to substance1
arsenic disulfidedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
perfluorohexanesulfonic aciddecreases expression1
abrineincreases expression1
dorsomorphindecreases expression, affects cotreatment1
PCI 5002affects cotreatment, increases expression1
Leflunomidedecreases expression1
Copperaffects binding, decreases expression1
Disulfiramaffects binding, decreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Methyl Methanesulfonateincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Zincaffects cotreatment, increases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.