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Atlas / Gene / ZFP28

ZFP28

gene
On this page

Also known as KIAA1431mkr5

Summary

ZFP28 (ZFP28 zinc finger protein, HGNC:17801) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 28 homolog (Q8NHY6). 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 140612 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 93 total
  • MANE Select transcript: NM_020828

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17801
Approved symbolZFP28
NameZFP28 zinc finger protein
Location19q13.43
Locus typegene with protein product
StatusApproved
AliasesKIAA1431, mkr5
Ensembl geneENSG00000196867
Ensembl biotypeprotein_coding
OMIM616798
Entrez140612

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000301318, ENST00000588163, ENST00000589836, ENST00000591844, ENST00000594386, ENST00000955594

RefSeq mRNA: 2 — MANE Select: NM_020828 NM_001308440, NM_020828

CCDS: CCDS12946, CCDS77363

Canonical transcript exons

ENST00000301318 — 8 exons

ExonStartEnd
ENSE000007286745653894856539226
ENSE000007286865654780756547902
ENSE000007286905654895856549121
ENSE000007286955655006756550181
ENSE000007287015655051056550605
ENSE000012905965655368456556808
ENSE000024971335654750856547634
ENSE000034819625653962556539716

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 87.32.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534387.32gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.97gold quality
tibialis anteriorUBERON:000138583.04gold quality
ganglionic eminenceUBERON:000402382.56gold quality
C1 segment of cervical spinal cordUBERON:000646982.06gold quality
calcaneal tendonUBERON:000370181.96gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.81gold quality
left ovaryUBERON:000211981.75gold quality
Brodmann (1909) area 9UBERON:001354081.53gold quality
tendonUBERON:000004381.50gold quality
cerebellar hemisphereUBERON:000224581.36gold quality
ventricular zoneUBERON:000305381.33gold quality
cerebellar cortexUBERON:000212981.23gold quality
right hemisphere of cerebellumUBERON:001489080.97gold quality
right ovaryUBERON:000211880.93gold quality
tibial arteryUBERON:000761080.91gold quality
popliteal arteryUBERON:000225080.89gold quality
anterior cingulate cortexUBERON:000983580.68gold quality
prefrontal cortexUBERON:000045180.44gold quality
hypothalamusUBERON:000189880.23gold quality
right frontal lobeUBERON:000281080.18gold quality
cerebellumUBERON:000203779.86gold quality
spinal cordUBERON:000224079.83gold quality
medial globus pallidusUBERON:000247779.75gold quality
aortaUBERON:000094779.63gold quality
descending thoracic aortaUBERON:000234579.35gold quality
tibial nerveUBERON:000132379.19gold quality
adenohypophysisUBERON:000219679.11gold quality
mucosa of stomachUBERON:000119978.99gold quality
tendon of biceps brachiiUBERON:000818878.90gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no5.62

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA2489.1ZFP28More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

68 targeting ZFP28, 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-4262100.0073.263931
HSA-MIR-428299.9975.366408
HSA-MIR-524-5P99.9873.434882
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-335-3P99.9373.364958
HSA-MIR-130599.9171.433443
HSA-MIR-367199.9073.043897
HSA-MIR-153-5P99.8973.866317
HSA-MIR-7845-5P99.8864.88771
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-132399.8369.892471
HSA-MIR-489-3P99.8066.46839
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-1212499.6869.172700
HSA-MIR-447099.6669.351767
HSA-MIR-561-3P99.6470.903647
HSA-MIR-1212299.5669.331672
HSA-MIR-1252-3P99.5567.712862
HSA-MIR-4761-5P99.5166.69804
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-444199.4966.563216
HSA-MIR-57899.4668.361787
HSA-MIR-132499.4666.571302
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-548AV-3P99.4368.501721
HSA-MIR-513A-3P99.3970.633620

Literature-anchored findings (GeneRIF, showing 2)

  • Characterization of ZFP28 and its role in human development (PMID:12127974)
  • these results suggest that murine and human Zfp28/ZFP28 is correlated with the pathogenesis of melanoma. (PMID:19329283)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp28ENSMUSG00000062861
rattus_norvegicusZfp28ENSRNOG00000042777

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 28 homolog — Q8NHY6 (reviewed: Q8NHY6)

Alternative names: Krueppel-like zinc finger factor X6

All UniProt accessions (2): Q8NHY6, K7EL00

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation. May have a role in embryonic development.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8NHY6-11yes
Q8NHY6-22

RefSeq proteins (2): NP_001295369, NP_065879* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050752C2H2-ZF_domainFamily

Pfam: PF00096, PF01352, PF13912

UniProt features (77 total): strand 28, zinc finger region 15, helix 15, turn 7, sequence conflict 4, domain 2, splice variant 2, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
2EM2SOLUTION NMR
2EM3SOLUTION NMR
2EM4SOLUTION NMR
2EMJSOLUTION NMR
2EMKSOLUTION NMR
2EMLSOLUTION NMR
2EN9SOLUTION NMR
2ENHSOLUTION NMR
2EOHSOLUTION NMR
2EP0SOLUTION NMR
2EPXSOLUTION NMR
2EPZSOLUTION NMR
2YTMSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NHY6-F158.760.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 90 (showing top): GGAMTNNNNNTCCY_UNKNOWN, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, FREAC3_01, TGANTCA_AP1_C, MODULE_544, SANSOM_APC_MYC_TARGETS, ZHENG_GLIOBLASTOMA_PLASTICITY_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, PLASARI_TGFB1_TARGETS_10HR_DN, MODULE_481, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

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

GO Molecular Function (5): 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), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

486 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZFP28TP53BP1Q12888566
ZFP28DPEP1P16444359
ZFP28LYL1P12980358
ZFP28TMEM182Q6ZP80357
ZFP28ZDHHC12Q96GR4355
ZFP28IGF2RP11717353
ZFP28TRAM1L1Q8N609351
ZFP28RUNDC3BQ96NL0343
ZFP28STX8Q9UNK0321
ZFP28CCDC43Q96MW1301
ZFP28G5EA03G5EA03282
ZFP28RFTN2Q52LD8279
ZFP28C2CD4CQ8TF44277
ZFP28LINGO3P0C6S8272
ZFP28MAFKO60675268

IntAct

7 interactions, top by confidence:

ABTypeScore
C8orf33ZFP28psi-mi:“MI:0915”(physical association)0.370
HMOX2ZFP28psi-mi:“MI:0915”(physical association)0.370
PPP2CBZFP28psi-mi:“MI:0915”(physical association)0.370
ZFP28PRKRApsi-mi:“MI:0915”(physical association)0.370
ZFP28KDM1Apsi-mi:“MI:0915”(physical association)0.370
Mpsi-mi:“MI:0914”(association)0.350

BioGRID (7): ZFP28 (Cross-Linking-MS (XL-MS)), ZFP28 (Affinity Capture-RNA), ZFP28 (Two-hybrid), ZFP28 (Two-hybrid), ZFP28 (Two-hybrid), ZFP28 (Two-hybrid), KDM1A (Two-hybrid)

ESM2 similar proteins: A2A761, A2T7D2, A3KN32, A3KN36, B2RUI1, D3ZVT0, E9PYI1, O43296, P10078, P17023, P17097, P17098, P52736, P59923, Q07231, Q14592, Q14929, Q16587, Q29RZ4, Q3TDE8, Q4V8A8, Q571J5, Q5CZA5, Q5JNZ3, Q5R741, Q5RB33, Q5RBX0, Q5RBY9, Q5RCD9, Q5VV52, Q61116, Q61967, Q62396, Q6A085, Q6PK81, Q6ZNG0, Q7Z398, Q8BI67, Q8BI99, Q8BIQ3

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance80
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1408 predictions. Top by Δscore:

VariantEffectΔscore
19:56539623:A:AGacceptor_gain1.0000
19:56539624:G:GAacceptor_gain1.0000
19:56539624:GCT:Gacceptor_gain1.0000
19:56539624:GCTC:Gacceptor_gain1.0000
19:56539624:GCTCT:Gacceptor_gain1.0000
19:56539714:CAGG:Cdonor_loss1.0000
19:56539715:AGGTG:Adonor_loss1.0000
19:56539716:GGT:Gdonor_loss1.0000
19:56539717:G:GAdonor_loss1.0000
19:56539717:G:GGdonor_gain1.0000
19:56539718:T:Adonor_loss1.0000
19:56547506:AG:Aacceptor_gain1.0000
19:56547507:GG:Gacceptor_gain1.0000
19:56547630:GCTGG:Gdonor_gain1.0000
19:56547633:GG:Gdonor_gain1.0000
19:56547634:GG:Gdonor_gain1.0000
19:56547635:G:GGdonor_gain1.0000
19:56547635:GTAAG:Gdonor_loss1.0000
19:56547636:TAAG:Tdonor_loss1.0000
19:56547805:A:AGacceptor_gain1.0000
19:56547806:G:GGacceptor_gain1.0000
19:56547900:CAGG:Cdonor_loss1.0000
19:56547904:T:Adonor_loss1.0000
19:56548947:AC:Aacceptor_gain1.0000
19:56548948:C:CAacceptor_gain1.0000
19:56548948:C:Gacceptor_gain1.0000
19:56548954:TCA:Tacceptor_loss1.0000
19:56548954:TCAGA:Tacceptor_gain1.0000
19:56548955:CAGAC:Cacceptor_gain1.0000
19:56548956:A:ACacceptor_loss1.0000

AlphaMissense

5716 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:56554154:T:CF457L0.999
19:56554156:T:AF457L0.999
19:56554156:T:GF457L0.999
19:56554238:T:CF485L0.999
19:56554240:C:AF485L0.999
19:56554240:C:GF485L0.999
19:56554325:T:CF514L0.999
19:56554327:C:AF514L0.999
19:56554327:C:GF514L0.999
19:56554493:T:CF570L0.999
19:56554495:C:AF570L0.999
19:56554495:C:GF570L0.999
19:56554512:T:CL576P0.999
19:56554520:C:GH579D0.999
19:56554522:T:AH579Q0.999
19:56554522:T:GH579Q0.999
19:56554577:T:CF598L0.999
19:56554579:T:AF598L0.999
19:56554579:T:GF598L0.999
19:56554604:C:GH607D0.999
19:56554606:T:AH607Q0.999
19:56554606:T:GH607Q0.999
19:56554661:T:CF626L0.999
19:56554663:C:AF626L0.999
19:56554663:C:GF626L0.999
19:56554745:T:CF654L0.999
19:56554747:C:AF654L0.999
19:56554747:C:GF654L0.999
19:56554829:T:CF682L0.999
19:56554831:C:AF682L0.999

dbSNP variants (sampled 300 via entrez): RS1000533175 (19:56552316 G>A,T), RS1000542410 (19:56551996 C>T), RS1000545468 (19:56535131 C>T), RS1000579526 (19:56535406 A>G), RS1000594671 (19:56551689 A>C), RS1000714670 (19:56540739 T>C), RS1000944174 (19:56539677 G>A,C), RS1001174732 (19:56546149 A>G), RS1001222751 (19:56551731 ATTCT>A), RS1001280631 (19:56534976 G>A), RS1001870894 (19:56540355 T>C,G), RS1002118516 (19:56547357 T>C), RS1002165652 (19:56539838 T>G), RS1002271362 (19:56552889 T>C), RS1002513928 (19:56537791 G>A)

Disease associations

OMIM: gene MIM:616798 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST010243_59Apolipoprotein B levels2.000000e-08
GCST90011900_168Serum alkaline phosphatase levels6.000000e-09
GCST90013406_71Liver enzyme levels (alkaline phosphatase)7.000000e-17

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004615apolipoprotein B measurement
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
Phenylmercuric Acetateaffects cotreatment, decreases expression2
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, decreases methylation1
arsenitedecreases expression, increases methylation1
sodium arsenitedecreases stability1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Arsenicincreases methylation1
Benzo(a)pyrenedecreases methylation, increases methylation1
Cisplatindecreases expression1
Testosteroneincreases expression1
Valproic Aciddecreases methylation1
Antirheumatic Agentsincreases 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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot