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ZFP64

gene
On this page

Also known as FLJ10734dJ831D17.1FLJ12628dJ548G19.1

Summary

ZFP64 (ZFP64 zinc finger protein, HGNC:15940) is a protein-coding gene on chromosome 20q13.2, encoding Zinc finger protein 64 (Q9NTW7). May be involved in the regulation of mesenchymal cell differentiation through transactivation of NOTCH1 target genes.

Predicted to enable DNA binding activity and zinc ion binding activity. Involved in mesenchymal cell differentiation. Located in cytoplasm and megasporocyte nucleus.

Source: NCBI Gene 55734 — RefSeq curated summary.

At a glance

  • GWAS associations: 21
  • Clinical variants (ClinVar): 158 total
  • MANE Select transcript: NM_018197

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15940
Approved symbolZFP64
NameZFP64 zinc finger protein
Location20q13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1
Ensembl geneENSG00000020256
Ensembl biotypeprotein_coding
OMIM618111
Entrez55734

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000216923, ENST00000346617, ENST00000361387, ENST00000371515, ENST00000371518, ENST00000371523, ENST00000395979, ENST00000395989, ENST00000456175, ENST00000461898, ENST00000467811, ENST00000477786, ENST00000904902, ENST00000959945

RefSeq mRNA: 5 — MANE Select: NM_018197 NM_001319146, NM_018197, NM_022088, NM_199426, NM_199427

CCDS: CCDS13439, CCDS13440, CCDS13441, CCDS13442, CCDS82630

Canonical transcript exons

ENST00000216923 — 6 exons

ExonStartEnd
ENSE000014554055215127852153428
ENSE000014554265219159152191779
ENSE000034802735216586452166025
ENSE000035231715216012352160374
ENSE000036472715218683252187071
ENSE000036590065216469552164757

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 93.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.5957 / max 127.4062, expressed in 1755 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
1879859.79811739
1879781.9356777
1879871.4111789
1879840.7342509
1879860.2277101
1879770.123145
1879800.123058
1879790.093237
1879880.089840
1879820.03868

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
germinal epithelium of ovaryUBERON:000130493.02gold quality
gingival epitheliumUBERON:000194992.93gold quality
secondary oocyteCL:000065591.93gold quality
palpebral conjunctivaUBERON:000181291.32gold quality
gingivaUBERON:000182890.89gold quality
parietal pleuraUBERON:000240090.60gold quality
pleuraUBERON:000097789.84gold quality
oocyteCL:000002389.61gold quality
squamous epitheliumUBERON:000691489.51gold quality
endothelial cellCL:000011589.32gold quality
visceral pleuraUBERON:000240189.29gold quality
hair follicleUBERON:000207389.11gold quality
epithelium of esophagusUBERON:000197688.88gold quality
esophagus squamous epitheliumUBERON:000692088.85gold quality
cervix squamous epitheliumUBERON:000692287.96gold quality
mammary ductUBERON:000176587.93gold quality
epithelium of mammary glandUBERON:000324487.92gold quality
epithelial cell of pancreasCL:000008387.88gold quality
tibiaUBERON:000097987.30gold quality
bronchial epithelial cellCL:000232887.18gold quality
nasal cavity epitheliumUBERON:000538487.13gold quality
penisUBERON:000098987.12gold quality
epithelium of nasopharynxUBERON:000195186.89gold quality
nasopharynxUBERON:000172886.88gold quality
colonic mucosaUBERON:000031786.81gold quality
metanephric glomerulusUBERON:000473686.56gold quality
renal glomerulusUBERON:000007486.33gold quality
mucosa of sigmoid colonUBERON:000499386.12gold quality
mucosa of paranasal sinusUBERON:000503086.06gold quality
pigmented layer of retinaUBERON:000178286.02gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no5.31

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

TargetRegulation
CDKN2A
IFNB1Repression
IL6Repression
NOTCH1
TNFActivation

Upstream regulators (CollecTRI, top): RUNX2

miRNA regulators (miRDB)

53 targeting ZFP64, 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-3163100.0077.238605
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-428299.9975.366408
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-56899.9869.862084
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-380-3P99.8970.181978
HSA-MIR-153-5P99.8973.866317
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-130399.6569.771662
HSA-MIR-10393-5P99.6568.011368
HSA-MIR-570099.6469.882280
HSA-MIR-6848-3P99.6466.49885
HSA-MIR-426199.5970.303415
HSA-MIR-7106-5P99.5367.473574

Literature-anchored findings (GeneRIF, showing 4)

  • Data indicate zinc finger protein 64 (ZFP64) as an essential transcription factor in mixed-lineage leukemia protein (MLL)-rearranged leukemia. (PMID:30503706)
  • Function and mechanism exploration of zinc finger protein 64 in lung adenocarcinoma cell growth and metastasis. (PMID:33054540)
  • ZFP64::NCOA3 gene fusion defines a novel subset of spindle cell rhabdomyosarcoma. (PMID:35521817)
  • ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer. (PMID:35843097)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriozfp64ENSDARG00000061147
mus_musculusZfp64ENSMUSG00000027551
rattus_norvegicusZfp93ENSRNOG00000012762
drosophila_melanogasterwekFBGN0001990
drosophila_melanogasterkmgFBGN0032473
drosophila_melanogasterCG17568FBGN0032763
drosophila_melanogasterCG10366FBGN0032814
drosophila_melanogasterCG8388FBGN0034062
drosophila_melanogasterCG4282FBGN0034114
drosophila_melanogasterCG4707FBGN0035036
drosophila_melanogasterCG6254FBGN0037794
drosophila_melanogasterCG9932FBGN0262160

Paralogs (1): ZNF335 (ENSG00000198026)

Protein

Protein identifiers

Zinc finger protein 64 — Q9NTW7 (reviewed: Q9NTW7)

Alternative names: Zinc finger protein 338

All UniProt accessions (4): A2A2N5, A2A2N6, Q9NTW7, H0Y669

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the regulation of mesenchymal cell differentiation through transactivation of NOTCH1 target genes.

Subunit / interactions. Interacts with ZNF70; this interaction promote the transactivation of the HES1 gene. Interacts with NOTCH1.

Subcellular location. Nucleus.

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

Isoforms (6)

UniProt IDNamesCanonical?
Q9NTW7-13yes
Q9NTW7-24, ZNF338
Q9NTW7-35
Q9NTW7-46
Q9NTW7-51
Q9NTW7-62

RefSeq proteins (5): NP_001306075, NP_060667, NP_071371, NP_955458, NP_955459 (=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050636C2H2-ZF_domain-containingFamily

Pfam: PF00096

UniProt features (57 total): zinc finger region 13, strand 11, splice variant 8, helix 7, sequence variant 6, compositionally biased region 3, region of interest 2, sequence conflict 2, cross-link 2, chain 1, turn 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
1X5WSOLUTION NMR
2DMDSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NTW7-F164.780.01

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): 545, 286, 397

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 124 (showing top): MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_MESENCHYMAL_CELL_DIFFERENTIATION, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_MESENCHYME_DEVELOPMENT, MCCLUNG_COCAINE_REWARD_5D, JACKSON_DNMT1_TARGETS_UP, VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP, SANSOM_APC_MYC_TARGETS, SCGGAAGY_ELK1_02, KIM_WT1_TARGETS_DN, MGGAAGTG_GABP_B, NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN

GO Biological Process (3): positive regulation of transcription by RNA polymerase II (GO:0045944), mesenchymal cell differentiation (GO:0048762), regulation of gene expression (GO:0010468)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), megasporocyte nucleus (GO:0043076)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
cell differentiation1
mesenchyme development1
gene expression1
regulation of macromolecule biosynthetic process1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
nucleus1

Protein interactions and networks

STRING

1008 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZFP64TRPS1Q9UHF7556
ZFP64RUNX3Q13761544
ZFP64NOTCH1P46531504
ZFP64MMP13P45452425
ZFP64TMEM240Q5SV17419
ZFP64SIK3Q9Y2K2407
ZFP64CFAP20DCQ6ZVT6400
ZFP64TSHZ2Q9NRE2400
ZFP64BCAS4Q8TDM0397
ZFP64SEC16BQ96JE7397
ZFP64IHHQ14623396
ZFP64KRTAP19-7Q3SYF9396
ZFP64PLEKHN1Q494U1396
ZFP64SPP1P10451390
ZFP64TMEM18Q96B42388

IntAct

102 interactions, top by confidence:

ABTypeScore
ZFP64FHL2psi-mi:“MI:0915”(physical association)0.740
FHL2ZFP64psi-mi:“MI:0915”(physical association)0.740
ZFP64LNX1psi-mi:“MI:0915”(physical association)0.670
AENZFP64psi-mi:“MI:0915”(physical association)0.670
ZFP64AENpsi-mi:“MI:0915”(physical association)0.670
ZFP64TRIM41psi-mi:“MI:0915”(physical association)0.670
TRIM41ZFP64psi-mi:“MI:0915”(physical association)0.670
LNX1ZFP64psi-mi:“MI:0915”(physical association)0.670
LMO2ZFP64psi-mi:“MI:0915”(physical association)0.560
ZFP64MFAP1psi-mi:“MI:0915”(physical association)0.560
ZFP64BYSLpsi-mi:“MI:0915”(physical association)0.560
BYSLZFP64psi-mi:“MI:0915”(physical association)0.560

BioGRID (71): ZFP64 (Two-hybrid), ZFP64 (Two-hybrid), ZFP64 (Two-hybrid), ZFP64 (Two-hybrid), PBK (Two-hybrid), AEN (Two-hybrid), LNX1 (Two-hybrid), TRIM41 (Two-hybrid), FAM124A (Two-hybrid), ZFP64 (Affinity Capture-MS), ZFP64 (Two-hybrid), BEGAIN (Two-hybrid), AEN (Two-hybrid), TRIM41 (Two-hybrid), ZFP64 (Affinity Capture-MS)

ESM2 similar proteins: A1L1J6, B1H2Q6, G5E8B9, O08954, O43167, O43623, O43829, O62836, O95625, P08044, P08048, P08155, P10925, P15619, P17010, P17012, P20385, P20662, P60319, P97469, Q01611, Q08376, Q13105, Q17895, Q20082, Q22024, Q25C93, Q3MHQ4, Q3U3I9, Q52V16, Q5DU09, Q5SVQ8, Q60821, Q6B4Z5, Q804Q5, Q811F1, Q8I7Z8, Q8N9L1, Q8TF68, Q90625

Diamond homologs: A0A1V6NWD3, A1L2U9, B0X9H6, B0XS89, B1WAZ8, B1WBU4, C8VJW0, G5EBU4, J9VX63, O60315, P10925, P15822, P20662, P31629, P36197, P52739, P53243, P56270, P56670, P56671, P78871, P80944, Q00453, Q00900, Q01611, Q03172, Q0IH98, Q0VCJ6, Q12132, Q29419, Q2I689, Q3UHF7, Q4WXK4, Q5JPB2, Q5RAU9, Q60542, Q62947, Q64318, Q6IQX8, Q6P882

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance139
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1997 predictions. Top by Δscore:

VariantEffectΔscore
20:52088386:ACTC:Adonor_loss1.0000
20:52088387:CTCA:Cdonor_loss1.0000
20:52088388:TCACC:Tdonor_loss1.0000
20:52088389:CACCC:Cdonor_loss1.0000
20:52088390:A:ACdonor_gain1.0000
20:52088390:AC:Adonor_gain1.0000
20:52088391:C:CAdonor_loss1.0000
20:52088391:C:CCdonor_gain1.0000
20:52088391:CC:Cdonor_gain1.0000
20:52088391:CCCG:Cdonor_gain1.0000
20:52088391:CCCGT:Cdonor_gain1.0000
20:52088654:A:Cacceptor_gain1.0000
20:52097368:CCTA:Cdonor_loss1.0000
20:52097369:CTA:Cdonor_loss1.0000
20:52097370:TA:Tdonor_loss1.0000
20:52097371:A:ACdonor_gain1.0000
20:52097371:AC:Adonor_gain1.0000
20:52097372:C:CCdonor_gain1.0000
20:52097372:CC:Cdonor_gain1.0000
20:52097432:CAAC:Cacceptor_gain1.0000
20:52097435:CCTAG:Cacceptor_loss1.0000
20:52097436:C:CAacceptor_loss1.0000
20:52097436:C:CCacceptor_gain1.0000
20:52097437:T:Aacceptor_loss1.0000
20:52098432:TCTTA:Tdonor_loss1.0000
20:52098433:CTTAC:Cdonor_loss1.0000
20:52098434:TTACC:Tdonor_loss1.0000
20:52098435:TA:Tdonor_loss1.0000
20:52098436:A:Tdonor_loss1.0000
20:52098437:C:CGdonor_loss1.0000

AlphaMissense

4532 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:52160149:A:GL246P1.000
20:52160180:A:GC236R1.000
20:52160189:A:GC233R1.000
20:52160223:G:CH221Q1.000
20:52160223:G:TH221Q1.000
20:52160225:G:CH221D1.000
20:52160233:A:GL218P1.000
20:52160273:A:GC205R1.000
20:52160307:G:CH193Q1.000
20:52160307:G:TH193Q1.000
20:52160309:G:CH193D1.000
20:52160334:A:CF184L1.000
20:52160334:A:TF184L1.000
20:52160336:A:GF184L1.000
20:52160348:A:GC180R1.000
20:52160357:A:GC177R1.000
20:52164699:G:CH169Q1.000
20:52164699:G:TH169Q1.000
20:52164701:G:CH169D1.000
20:52164711:A:CH165Q1.000
20:52164711:A:TH165Q1.000
20:52164713:G:CH165D1.000
20:52164713:G:TH165N1.000
20:52160137:A:GL250P0.999
20:52160139:G:CH249Q0.999
20:52160139:G:TH249Q0.999
20:52160141:G:CH249D0.999
20:52160141:G:TH249N0.999
20:52160166:G:CS240R0.999
20:52160166:G:TS240R0.999

dbSNP variants (sampled 300 via entrez): RS1000010681 (20:52101852 C>T), RS1000062976 (20:52101717 T>A,G), RS1000125947 (20:52189437 CAGATCAT>C), RS1000133287 (20:52105670 C>G,T), RS1000136706 (20:52187860 C>T), RS1000197566 (20:52189208 G>A,C), RS1000199441 (20:52106967 G>A), RS1000206153 (20:52123466 C>G,T), RS1000225255 (20:52166796 G>T), RS1000267493 (20:52087911 G>A,C,T), RS1000285181 (20:52161258 T>C,G), RS1000327867 (20:52155936 C>G,T), RS1000369339 (20:52154591 A>T), RS1000401058 (20:52161072 G>A), RS1000403085 (20:52156164 C>T)

Disease associations

OMIM: gene MIM:618111 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

StudyTraitp-value
GCST000013_5Amyotrophic lateral sclerosis5.000000e-06
GCST001521_14Subcutaneous adipose tissue5.000000e-06
GCST002783_119Body mass index2.000000e-11
GCST002783_144Body mass index8.000000e-08
GCST002783_331Body mass index2.000000e-08
GCST003059_22Parkinson’s disease1.000000e-06
GCST004064_29Waist-hip ratio2.000000e-08
GCST004064_32Waist-hip ratio9.000000e-06
GCST004065_104Waist circumference1.000000e-08
GCST004065_90Waist circumference2.000000e-09
GCST004068_18Venous thromboembolism adjusted for sickle cell variant rs77121243-T8.000000e-06
GCST004401_7Reading disability or specific language impairment (pleiotropy)6.000000e-06
GCST004495_87BMI (adjusted for smoking behaviour)1.000000e-06
GCST004497_65Body mass index (joint analysis main effects and smoking interaction)3.000000e-06
GCST004499_80BMI in non-smokers4.000000e-06
GCST004904_208Body mass index5.000000e-13
GCST005651_9Urinary metabolite levels in chronic kidney disease3.000000e-08
GCST005830_60Hand grip strength2.000000e-08
GCST010242_256HDL cholesterol levels1.000000e-09
GCST010988_328Adult body size3.000000e-19
GCST90000025_690Appendicular lean mass5.000000e-13

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004343waist-hip ratio
EFO:0004318smoking behavior
EFO:0005116urinary metabolite measurement
EFO:0006941grip strength measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, affects methylation3
Valproic Acidincreases expression, affects expression, decreases expression3
Tretinoindecreases expression2
TAK-243increases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2affects methylation1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediaminedecreases expression1
di-n-butylphosphoric acidaffects expression1
entinostatincreases expression1
abrinedecreases expression1
bisphenol Sdecreases methylation1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Azacitidineaffects methylation1
Cisplatinincreases expression, affects cotreatment1
Doxorubicindecreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Methapyrileneincreases methylation1
Ozoneincreases abundance, affects expression1
Phthalic Acidsdecreases methylation1
Tobacco Smoke Pollutiondecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_HD08HEK293 eGFP-ZFP64Transformed cell lineFemale

Clinical trials (associated diseases)

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

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
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BioBTree
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Sources 74

This page pulls from 74 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_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot