ZFP1

gene
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Also known as PITAFLJ34243ZNF475

Summary

ZFP1 (ZFP1 zinc finger protein, HGNC:23328) is a protein-coding gene on chromosome 16q23.1, encoding Zinc finger protein 1 homolog (Q6P2D0). May be involved in transcriptional regulation.

This gene belongs to the zinc finger protein family. Some members of this family bind to DNA by zinc-mediated secondary structures called zinc fingers, and are involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 162239 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 71 total
  • MANE Select transcript: NM_153688

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23328
Approved symbolZFP1
NameZFP1 zinc finger protein
Location16q23.1
Locus typegene with protein product
StatusApproved
AliasesPITA, FLJ34243, ZNF475
Ensembl geneENSG00000184517
Ensembl biotypeprotein_coding
OMIM617230
Entrez162239

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000332307, ENST00000393430, ENST00000464850, ENST00000563356, ENST00000564989, ENST00000566105, ENST00000567481, ENST00000568079, ENST00000570010, ENST00000870669, ENST00000870670, ENST00000870671, ENST00000931429

RefSeq mRNA: 8 — MANE Select: NM_153688 NM_001318469, NM_001318471, NM_001318472, NM_001318473, NM_001318474, NM_001318475, NM_001318476, NM_153688

CCDS: CCDS10914, CCDS82012, CCDS82013

Canonical transcript exons

ENST00000570010 — 4 exons

ExonStartEnd
ENSE000026058797514852475148643
ENSE000026206537516925375172234
ENSE000034835717516677075166896
ENSE000036347387515290975152966

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7677 / max 117.4642, expressed in 1746 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15501611.76771746

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534392.74gold quality
ganglionic eminenceUBERON:000402390.06gold quality
ventricular zoneUBERON:000305387.88gold quality
superior frontal gyrusUBERON:000266187.13gold quality
prefrontal cortexUBERON:000045186.03gold quality
primary visual cortexUBERON:000243685.26gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.23gold quality
frontal cortexUBERON:000187084.14gold quality
Brodmann (1909) area 9UBERON:001354083.71gold quality
corpus callosumUBERON:000233683.49gold quality
dorsolateral prefrontal cortexUBERON:000983483.41gold quality
cerebral cortexUBERON:000095683.33gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.94gold quality
anterior cingulate cortexUBERON:000983582.49gold quality
liverUBERON:000210782.24gold quality
islet of LangerhansUBERON:000000682.23gold quality
nucleus accumbensUBERON:000188281.67gold quality
right lobe of liverUBERON:000111481.65gold quality
amygdalaUBERON:000187681.28gold quality
temporal lobeUBERON:000187181.24gold quality
caudate nucleusUBERON:000187380.91gold quality
right frontal lobeUBERON:000281080.91gold quality
endometriumUBERON:000129580.88gold quality
brainUBERON:000095580.82gold quality
putamenUBERON:000187480.62gold quality
smooth muscle tissueUBERON:000113580.60gold quality
Ammon’s hornUBERON:000195480.53gold quality
calcaneal tendonUBERON:000370180.35gold quality
skeletal muscle tissueUBERON:000113480.25gold quality
right coronary arteryUBERON:000162579.64gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.29

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
CD74
ERVW-4
SLC11A1

Upstream regulators (CollecTRI, top): PRDM1, STAT1

miRNA regulators (miRDB)

100 targeting ZFP1, 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-7110-3P100.0073.182486
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-8485100.0077.574731
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-806899.9873.852376
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-433-3P99.9869.371203
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-545-3P99.9570.742783
HSA-MIR-651-3P99.9473.485177
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-338-5P99.9272.342951
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-129-5P99.8870.263273
HSA-MIR-612499.8769.783551
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-394199.8670.542735
HSA-MIR-5010-3P99.8370.602357

Literature-anchored findings (GeneRIF, showing 1)

  • ZFP1 is a biomarker related to poor prognosis and immunity in gastric cancer. (PMID:39261568)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp1ENSMUSG00000055835
rattus_norvegicusZfp1ENSRNOG00000019059

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 1 homologQ6P2D0 (reviewed: Q6P2D0)

Alternative names: Zinc finger protein 475

All UniProt accessions (4): Q6P2D0, H3BM94, H3BV40, J3KNQ1

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 IDNamesCanonical?
Q6P2D0-11yes
Q6P2D0-22

RefSeq proteins (8): NP_001305398, NP_001305400, NP_001305401, NP_001305402, NP_001305403, NP_001305404, NP_001305405, NP_710155* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF01352

UniProt features (16 total): zinc finger region 8, cross-link 3, region of interest 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6P2D0-F165.560.29

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): 74, 114, 145

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 172 (showing top): GGAMTNNNNNTCCY_UNKNOWN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, SANSOM_APC_TARGETS, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, SWEET_LUNG_CANCER_KRAS_UP, WONG_ADULT_TISSUE_STEM_MODULE, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, chr16q23, ESC_V6.5_UP_LATE.V1_DN

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), sequence-specific double-stranded DNA binding (GO:1990837), 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
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
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

510 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZFP1CASZ1Q86V15893
ZFP1MYCP01106726
ZFP1CDKN1AP38936605
ZFP1PRDM2Q13029589
ZFP1DOT1LQ8TEK3505
ZFP1CIZ1Q9ULV3505
ZFP1ZPR1O75312472
ZFP1SPRR1BP22528470
ZFP1COMMD9Q9P000455
ZFP1GATMP50440445
ZFP1TRMT11Q7Z4G4429
ZFP1DIRAS1O95057427
ZFP1KLK7P49862426
ZFP1PLEKHF1Q96S99398
ZFP1GEMIN5Q8TEQ6386
ZFP1KLK6Q92876386

IntAct

88 interactions, top by confidence:

ABTypeScore
KRT31HGSpsi-mi:“MI:0914”(association)0.780
IPO8TRIM28psi-mi:“MI:0914”(association)0.640
AKR1C2AKR1C4psi-mi:“MI:0914”(association)0.640
ZFP1MAP3K20psi-mi:“MI:0915”(physical association)0.600
ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1TSPYL2psi-mi:“MI:0915”(physical association)0.560
LDOC1ZFP1psi-mi:“MI:0915”(physical association)0.560
KRT40ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1CCDC125psi-mi:“MI:0915”(physical association)0.560
ZFP1CEP70psi-mi:“MI:0915”(physical association)0.560
ZFP1CARD10psi-mi:“MI:0915”(physical association)0.560
HAP1ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1CRLF3psi-mi:“MI:0915”(physical association)0.560
MTUS2ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1TBC1D1psi-mi:“MI:0915”(physical association)0.560
ZFP1HOOK2psi-mi:“MI:0915”(physical association)0.560
GOLGA6L9ZFP1psi-mi:“MI:0915”(physical association)0.560
CAVIN1ZFP1psi-mi:“MI:0915”(physical association)0.560
POU6F2ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1CEP19psi-mi:“MI:0915”(physical association)0.560
EMDZFP1psi-mi:“MI:0915”(physical association)0.560
ZNF250ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1CIB3psi-mi:“MI:0915”(physical association)0.560
MFAP1ZFP1psi-mi:“MI:0915”(physical association)0.560
ZFP1TRIM41psi-mi:“MI:0915”(physical association)0.560
TRIM28ZNF316psi-mi:“MI:0914”(association)0.530
TRIM28ZNF320psi-mi:“MI:0914”(association)0.530
SERTAD4POTEFpsi-mi:“MI:0914”(association)0.530
WASHC3WASH3Ppsi-mi:“MI:0914”(association)0.530

BioGRID (66): ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Affinity Capture-MS), ZFP1 (Two-hybrid), ZFP1 (Two-hybrid), ZFP1 (Two-hybrid), ZFP1 (Two-hybrid), ZFP1 (Two-hybrid), ZFP1 (Two-hybrid)

ESM2 similar proteins: A0JPL0, A3KN36, A7MBI1, A8MT65, B2RXC5, D3ZVT0, P08042, P21506, P51508, P52738, Q02525, Q06730, Q12901, Q2KI58, Q2M218, Q2M3W8, Q2M3X9, Q2VY69, Q49AA0, Q4R6J4, Q4V8A8, Q5FWF6, Q5HY98, Q5RB33, Q5RC79, Q5REF1, Q5T5D7, Q5VIY5, Q61967, Q6P2D0, Q6ZN11, Q86XU0, Q86Y25, Q8N782, Q8N859, Q8NB42, Q8TF39, Q8TF47, Q8WXB4, Q95K49

Diamond homologs: A0JPL0, A2VDP4, A6QLU5, A6QPT6, A8MQ14, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, P08042, P0CH99, P0CI00, P17014, P17025, P17030, P17031, P17032, P17098, P21506, P51508, P51523, P51786, P51814, P52736, P52738, Q02525, Q03923, Q03936, Q06730, Q06732, Q0VCB0, Q13401, Q14587, Q16587, Q2M218, Q2M3X9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance62
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1075 predictions. Top by Δscore:

VariantEffectΔscore
16:75148645:T:Adonor_loss1.0000
16:75152907:A:AGacceptor_gain1.0000
16:75152908:G:GAacceptor_gain1.0000
16:75152908:GTT:Gacceptor_gain1.0000
16:75152908:GTTCT:Gacceptor_gain1.0000
16:75166893:GTGG:Gdonor_gain1.0000
16:75152902:A:AGacceptor_gain0.9900
16:75152904:TCCA:Tacceptor_loss0.9900
16:75152906:CAGTT:Cacceptor_loss0.9900
16:75152908:G:Aacceptor_loss0.9900
16:75152908:GT:Gacceptor_gain0.9900
16:75152908:GTTC:Gacceptor_gain0.9900
16:75152964:CAGGT:Cdonor_loss0.9900
16:75152965:AGG:Adonor_loss0.9900
16:75152967:GT:Gdonor_loss0.9900
16:75152968:TGAGT:Tdonor_loss0.9900
16:75152969:GAGTT:Gdonor_loss0.9900
16:75169251:A:AGacceptor_gain0.9900
16:75169252:G:GGacceptor_gain0.9900
16:75169252:GAA:Gacceptor_gain0.9900
16:75169252:GAAGT:Gacceptor_gain0.9900
5:122151777:A:AGacceptor_gain0.9900
5:122151778:G:GGacceptor_gain0.9900
16:75149258:G:GAdonor_gain0.9800
16:75149268:G:GGdonor_gain0.9800
16:75166723:T:Gacceptor_gain0.9800
16:75169245:A:AGacceptor_gain0.9800
5:122129649:GCTC:Gdonor_gain0.9800
5:122151776:CAGA:Cacceptor_loss0.9800
5:122151777:A:ATacceptor_loss0.9800

AlphaMissense

2724 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:75169771:T:CF221L0.999
16:75169773:C:AF221L0.999
16:75169773:C:GF221L0.999
16:75169790:T:CL227P0.999
16:75169855:T:CF249L0.999
16:75169857:C:AF249L0.999
16:75169857:C:GF249L0.999
16:75170191:T:CF361L0.999
16:75170193:C:AF361L0.999
16:75170193:C:GF361L0.999
16:75170275:T:CF389L0.999
16:75170277:T:AF389L0.999
16:75170277:T:GF389L0.999
16:75169939:T:CF277L0.998
16:75169941:T:AF277L0.998
16:75169941:T:GF277L0.998
16:75169958:T:CL283P0.998
16:75170042:T:CL311P0.998
16:75170126:T:CL339P0.998
16:75170225:G:CR372P0.998
16:75169800:T:AH230Q0.997
16:75169800:T:GH230Q0.997
16:75169802:A:CQ231P0.997
16:75169874:T:CL255P0.997
16:75169968:C:AH286Q0.997
16:75169968:C:GH286Q0.997
16:75170054:A:CQ315P0.997
16:75170107:T:CF333L0.997
16:75170109:T:AF333L0.997
16:75170109:T:GF333L0.997

dbSNP variants (sampled 300 via entrez): RS1000068594 (16:75154179 G>A,T), RS1000083076 (16:75141748 A>C), RS1000148973 (16:75148470 C>A,G), RS1000179135 (16:75127065 T>C), RS1000228112 (16:75131535 G>A), RS1000269076 (16:75162377 G>A,T), RS1000284932 (16:75122540 G>A), RS1000322517 (16:75166058 A>G), RS1000412207 (16:75148557 C>CA), RS1000436101 (16:75136552 A>G), RS1000467084 (16:75118600 C>T), RS1000584335 (16:75117595 G>A,C), RS1000592617 (16:75139627 G>A,T), RS1000625267 (16:75144123 T>G), RS1000650239 (16:75171182 C>A,T)

Disease associations

OMIM: gene MIM:617230 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002553_10Pancreatic cancer1.000000e-10
GCST004860_122Alcoholic chronic pancreatitis4.000000e-09
GCST004860_124Alcoholic chronic pancreatitis8.000000e-07
GCST004860_136Alcoholic chronic pancreatitis2.000000e-06
GCST004860_62Alcoholic chronic pancreatitis5.000000e-06
GCST90002382_445Eosinophil percentage of white cells2.000000e-10
GCST90002388_172Lymphocyte count4.000000e-13

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007991eosinophil percentage of leukocytes
EFO:0004587lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation3
Phenylmercuric Acetateaffects cotreatment, decreases expression2
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Acroleindecreases expression, increases abundance, affects cotreatment1
Air Pollutantsaffects cotreatment, decreases expression, increases abundance1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Ozoneaffects cotreatment, decreases expression, increases abundance1
Phthalic Acidsdecreases methylation1
Urethanedecreases expression1
Copper Sulfatedecreases expression1
Particulate Matterincreases expression1
Volatile Organic Compoundsaffects cotreatment, decreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): alcoholic pancreatitis