ZFP42

gene
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Also known as REX1ZNF754

Summary

ZFP42 (ZFP42 zinc finger protein, HGNC:30949) is a protein-coding gene on chromosome 4q35.2, encoding Zinc finger protein 42 homolog (Q96MM3). Involved in the reprogramming of X-chromosome inactivation during the acquisition of pluripotency.

Enables sequence-specific double-stranded DNA binding activity. Involved in female gonad development and male gonad development. Located in cytoplasm.

Source: NCBI Gene 132625 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 64 total — 1 pathogenic
  • Transcription factor: yes — 21 downstream targets (CollecTRI)
  • MANE Select transcript: NM_174900

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30949
Approved symbolZFP42
NameZFP42 zinc finger protein
Location4q35.2
Locus typegene with protein product
StatusApproved
AliasesREX1, ZNF754
Ensembl geneENSG00000179059
Ensembl biotypeprotein_coding
OMIM614572
Entrez132625

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 26 protein_coding

ENST00000326866, ENST00000509524, ENST00000618147, ENST00000940024, ENST00000940025, ENST00000940026, ENST00000940027, ENST00000940028, ENST00000940029, ENST00000940030, ENST00000940031, ENST00000940032, ENST00000940033, ENST00000940034, ENST00000940035, ENST00000940036, ENST00000940037, ENST00000940038, ENST00000940039, ENST00000940040, ENST00000940041, ENST00000940042, ENST00000940043, ENST00000940044, ENST00000940045, ENST00000940046

RefSeq mRNA: 2 — MANE Select: NM_174900 NM_001304358, NM_174900

CCDS: CCDS3849

Canonical transcript exons

ENST00000326866 — 4 exons

ExonStartEnd
ENSE00001515523187999609187999685
ENSE00001515525187999108187999273
ENSE00001515526187995771187995840
ENSE00002020347188002713188005046

Expression profiles

Bgee: expression breadth broad, 33 present calls, max score 88.18.

FANTOM5 (CAGE): breadth broad, TPM avg 3.9185 / max 289.9133, expressed in 202 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
509273.8523200
509290.066232

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233688.18gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.73gold quality
amniotic fluidUBERON:000017376.58gold quality
spermCL:000001974.71silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047373.81gold quality
tendon of biceps brachiiUBERON:000818866.04silver quality
placentaUBERON:000198757.64gold quality
testisUBERON:000047356.25gold quality
medial globus pallidusUBERON:000247755.83gold quality
right testisUBERON:000453455.64gold quality
left testisUBERON:000453354.41gold quality
cardiac muscle of right atriumUBERON:000337954.34gold quality
cartilage tissueUBERON:000241854.23silver quality
left ventricle myocardiumUBERON:000656654.23gold quality
pancreatic ductal cellCL:000207954.17silver quality
epithelial cell of pancreasCL:000008353.94gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
ileal mucosaUBERON:000033153.16silver quality
globus pallidusUBERON:000187552.45gold quality
tibialis anteriorUBERON:000138552.32silver quality
upper leg skinUBERON:000426251.25gold quality
ventricular zoneUBERON:000305351.11silver quality
myocardiumUBERON:000234950.25gold quality
deltoidUBERON:000147648.62gold quality
skin of hipUBERON:000155447.17silver quality
nasal cavity epitheliumUBERON:000538447.03gold quality
tendonUBERON:000004346.99gold quality
ganglionic eminenceUBERON:000402346.58silver quality
quadriceps femorisUBERON:000137746.52gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-6819yes411.11
E-MTAB-9388yes6.51
E-ANND-3yes4.11
E-MTAB-9801no2.56

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

21 targets.

TargetRegulation
AKT1
BDKRB2
BMP4
CCNB1Activation
CCNB2
DKK1
DPPA4
DPPA5
FGF4
LEFTY2
LIN28A
MAP2K3Unknown
MIR302AUnknown
PIK3R1
RLIM
SLU7
SOCS3
SPARC
THY1
UTF1
ZFP42Activation

JASPAR motifs

MotifNameFamily
MA1651.1ZFP42More than 3 adjacent zinc fingers
MA1651.2ZFP42More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28473536

Upstream regulators (CollecTRI, top): NANOG, NR0B1, POU2F1, POU3F1, POU5F1, SOX2, YY1, ZFP42, ZNF263

miRNA regulators (miRDB)

40 targeting ZFP42, 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-1277-5P100.0073.955056
HSA-MIR-4425100.0067.591049
HSA-MIR-8485100.0077.574731
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3689D100.0066.141181
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-569699.9872.364487
HSA-MIR-767-5P99.9570.85993
HSA-MIR-335-3P99.9373.364958
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-607999.8468.541170
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-58799.6470.862611
HSA-MIR-443799.5265.291266
HSA-MIR-318299.4068.152454
HSA-MIR-148A-5P99.3068.271141
HSA-MIR-126499.2566.811317
HSA-MIR-4477B99.2370.491733
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-21-3P99.2168.951312
HSA-MIR-66199.0965.942062
HSA-MIR-316899.0867.751384

Literature-anchored findings (GeneRIF, showing 11)

  • MAPCs express the OCT4 and REX1 transcription factors, two specific markers of undifferentiated embryonic stem (ES) cells. (PMID:15790780)
  • REX1 functions in normal adult epithelial cells and tumorigenic stem cells. (PMID:16865673)
  • Data show that Oct-4, Rex-1, and Gata-4 expression in human mesenchymal stem cells increases cell differentiation efficiency but not hTERT expression. (PMID:17211834)
  • expression of REX-1 in meiotic cells from both testes and ovary indicate a role in meiosis. (PMID:18281244)
  • hRex1 binds to the hRex1 promoter region at -298 bp and positively regulates hRex1 transcription, but this regulation is lost in PC-3 human prostate cancer cells. (PMID:20232320)
  • reduced expression protein-1 (REX-1) is widely expressed in human skin and may be involved in cutaneous differentiation but not in stem cell fate determination. (PMID:21446939)
  • Results show that a novel pluripotency regulator, REX1, is essential for pluripotency and reprogramming. (PMID:23939908)
  • Results provide evidence that bFGF regulates stemness maintenance in stem cells isolated from human exfoliated deciduous teeth (SHEDs) by enhancing REX-1 mRNA expression via the FGFR and Akt signaling pathways. Moreover, IL-6 is also involved in the bFGF-induced REX1 expression. (PMID:27883224)
  • ZFP42 missense mutation was identified in patients with multilocus imprinting disturbances. ZFP42 pathogenic mutation affects protein conformation and activity. (PMID:30221575)
  • REX1 overexpression could play a crucial role in the metastasis and invasion of cervical cancer by upregulating the activity of the JAK2/STAT3 pathway by trans-suppressing SOCS1 expression. (PMID:31409905)
  • REX-1 Represses RASSF1a and Activates the MEK/ERK Pathway to Promote Tumorigenesis in Prostate Cancer. (PMID:34183450)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusZfp42ENSMUSG00000051176
rattus_norvegicusZfp42ENSRNOG00000063726
rattus_norvegicusZfp42ENSRNOG00000067356
drosophila_melanogasterpholFBGN0035997
caenorhabditis_elegansWBGENE00011639

Paralogs (2): YY1 (ENSG00000100811), YY2 (ENSG00000230797)

Protein

Protein identifiers

Zinc finger protein 42 homologQ96MM3 (reviewed: Q96MM3)

Alternative names: Reduced expression protein 1, Zinc finger protein 754

All UniProt accessions (1): Q96MM3

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the reprogramming of X-chromosome inactivation during the acquisition of pluripotency. Required for efficient elongation of TSIX, a non-coding RNA antisense to XIST. Binds DXPas34 enhancer within the TSIX promoter. Involved in ES cell self-renewal.

Subcellular location. Nucleus.

Tissue specificity. Expressed in kidney, epidermal keratinocytes, prostate epithelial cells, bronchial and small airway lung epithelial cells (at protein level). Expressed in malignant kidney and several carcinoma cell lines (at protein level). Expressed in embryonic stem cells, kidney, epidermal keratinocytes, prostate epithelial cells, bronchial and small airway lung epithelial cells. Expressed in embryonal carcinomas, seminomas, malignant kidney and several carcinoma cell lines.

Post-translational modifications. Polyubiquitinated by RNF12, leading to proteasomal degradation.

Induction. Down-regulated upon retinoic acid addition to F9 stem cells.

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

RefSeq proteins (2): NP_001291287, NP_777560* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096

UniProt features (10 total): zinc finger region 4, cross-link 2, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96MM3-F157.150.27

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 (2): 231, 233

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): LI_CISPLATIN_RESISTANCE_DN, MUELLER_PLURINET, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, chr4q35, GOBP_FEMALE_SEX_DIFFERENTIATION, GOBP_SEX_DIFFERENTIATION, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, CONRAD_STEM_CELL, YAMAZAKI_TCEB3_TARGETS_DN, GOBP_MALE_SEX_DIFFERENTIATION, GOBP_DEVELOPMENT_OF_PRIMARY_SEXUAL_CHARACTERISTICS, GOBP_MEIOTIC_CELL_CYCLE, GOCC_PCG_PROTEIN_COMPLEX, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), male gonad development (GO:0008584), female gonad development (GO:0008585), meiotic cell cycle (GO:0051321)

GO Molecular Function (8): 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), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): chromatin (GO:0000785), transcription regulator complex (GO:0005667), cytoplasm (GO:0005737), PcG protein complex (GO:0031519), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
gonad development2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
cellular anatomical structure2
transcription by RNA polymerase II1
development of primary male sexual characteristics1
development of primary female sexual characteristics1
cell cycle1
sexual reproduction1
reproductive process1
meiotic nuclear division1
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
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
chromosome1
protein-containing complex1
intracellular anatomical structure1
nuclear protein-containing complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1178 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZFP42NANOGQ9H9S0820
ZFP42ESRRBO95718724
ZFP42POU5F1P31359715
ZFP42DPPA3Q6W0C5696
ZFP42SOX2P48431694
ZFP42UTF1Q5T230665
ZFP42DPPA4Q7L190626
ZFP42RYBPQ8N488625
ZFP42TFCP2L1Q9NZI6624
ZFP42GDF3Q9NR23602
ZFP42TBX3O15119597
ZFP42DPPA2Q7Z7J5597
ZFP42CRIPTOP13385596
ZFP42DPPA5A6NC42593
ZFP42FBXO15Q8NCQ5585

IntAct

17 interactions, top by confidence:

ABTypeScore
MEOX2ZFP42psi-mi:“MI:0915”(physical association)0.560
PIAS2ZFP42psi-mi:“MI:0915”(physical association)0.560
LHX2ZFP42psi-mi:“MI:0915”(physical association)0.560
SUMO1ZFP42psi-mi:“MI:0915”(physical association)0.560
RNF4ZFP42psi-mi:“MI:0915”(physical association)0.560
ZFP42EEF1A2psi-mi:“MI:0914”(association)0.350
ZFP42MEOX2psi-mi:“MI:0915”(physical association)0.000
ZFP42PIAS2psi-mi:“MI:0915”(physical association)0.000
ZFP42LHX2psi-mi:“MI:0915”(physical association)0.000
ZFP42SUMO1psi-mi:“MI:0915”(physical association)0.000
ZFP42RNF4psi-mi:“MI:0915”(physical association)0.000

BioGRID (17): ZFP42 (Affinity Capture-MS), ZFP42 (Two-hybrid), ZFP42 (Two-hybrid), ZFP42 (Two-hybrid), ZFP42 (Two-hybrid), ZFP42 (Two-hybrid), ZFP42 (Affinity Capture-MS), ZFP42 (Affinity Capture-MS), AGO4 (Affinity Capture-MS), EEF1A2 (Affinity Capture-MS), ZFP42 (Affinity Capture-MS), PPIA (Cross-Linking-MS (XL-MS)), YAF2 (Two-hybrid), EED (Two-hybrid), RYBP (Two-hybrid)

ESM2 similar proteins: A0JPK3, A1YFX5, A2RQG7, A7KBS4, F4JUI3, G3X9G7, O49498, P03131, P04605, P04614, P05909, P0C1K0, P11332, P12453, P18098, P24109, P35965, P98182, Q09424, Q0VCB0, Q19203, Q2YDJ5, Q3UZB0, Q567C6, Q5BI31, Q5EXX3, Q5M948, Q62396, Q6AXY9, Q6PB60, Q6PI77, Q71HP2, Q74124, Q7JUR5, Q7Z142, Q7Z2Y5, Q80YD3, Q86UQ0, Q8C0P7, Q8C6P8

Diamond homologs: A0JC51, A2ANX9, O15391, O57311, O57415, O60481, O62836, O73689, O95409, P08048, P0C6P6, P10925, P17010, P17012, P18747, P20662, P22227, P25490, P34694, P46684, P80944, Q00899, Q10RP4, Q12145, Q15915, Q29419, Q2FAY8, Q3TTC2, Q3UH06, Q3US17, Q3Y4E1, Q52V16, Q5NVT2, Q5R782, Q5RJ54, Q61467, Q61624, Q62520, Q62521, Q62806

SIGNOR signaling

2 interactions.

AEffectBMechanism
POU5F1“up-regulates quantity by expression”ZFP42“transcriptional regulation”
RLIM“down-regulates quantity by destabilization”ZFP42ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance46
Likely benign7
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
979496GRCh37/hg19 4q35.2(chr4:187391214-190957473)x1Pathogenic

SpliceAI

526 predictions. Top by Δscore:

VariantEffectΔscore
4:187995838:GGG:Gdonor_gain1.0000
4:187995839:GGG:Gdonor_gain1.0000
4:187995839:GG:Gdonor_gain0.9900
4:187995840:GG:Gdonor_gain0.9900
4:187995841:G:GAdonor_loss0.9900
4:187995841:G:GGdonor_gain0.9900
4:187995842:T:Gdonor_loss0.9900
4:187999274:GT:Gdonor_gain0.9800
4:187995837:AGGG:Adonor_gain0.9600
4:187995838:GGGG:Gdonor_gain0.9600
4:187995836:CAGGG:Cdonor_gain0.9500
4:187995840:G:Tdonor_gain0.9500
4:187997716:G:GGdonor_gain0.9400
4:187999607:A:AGacceptor_gain0.9300
4:187999608:G:GGacceptor_gain0.9300
4:188001322:A:AGdonor_gain0.9300
4:188001323:G:GGdonor_gain0.9300
4:188002709:GCAGG:Gacceptor_loss0.9300
4:188002710:CAG:Cacceptor_loss0.9300
4:188002711:A:ACacceptor_loss0.9300
4:188002712:GGT:Gacceptor_gain0.9300
4:187997715:A:AGdonor_gain0.9200
4:188002702:T:Gacceptor_loss0.9200
4:188001319:T:TGdonor_gain0.8900
4:187999271:GAAGT:Gdonor_gain0.8800
4:188002701:A:AGacceptor_loss0.8800
4:187997505:GC:Gdonor_gain0.8700
4:187997653:A:Gacceptor_gain0.8700
4:188002709:G:GAacceptor_gain0.8600
4:188002708:A:AGacceptor_gain0.8200

AlphaMissense

2032 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:188003573:T:CF256L1.000
4:188003575:C:AF256L1.000
4:188003575:C:GF256L1.000
4:188003636:T:CC277R1.000
4:188003462:T:CC219R0.999
4:188003483:T:CF226L0.999
4:188003485:C:AF226L0.999
4:188003485:C:GF226L0.999
4:188003546:T:AC247S0.999
4:188003546:T:CC247R0.999
4:188003547:G:CC247S0.999
4:188003548:C:GC247W0.999
4:188003574:T:CF256S0.999
4:188003636:T:AC277S0.999
4:188003637:G:CC277S0.999
4:188003638:T:GC277W0.999
4:188003663:T:CF286L0.999
4:188003664:T:CF286S0.999
4:188003665:T:AF286L0.999
4:188003665:T:GF286L0.999
4:188003375:T:CC190R0.998
4:188003377:T:GC190W0.998
4:188003464:T:GC219W0.998
4:188003471:T:CC222R0.998
4:188003484:T:CF226S0.998
4:188003600:C:GH265D0.998
4:188003602:C:AH265Q0.998
4:188003602:C:GH265Q0.998
4:188003607:G:CR267P0.998
4:188003612:C:GH269D0.998

dbSNP variants (sampled 300 via entrez): RS1000017269 (4:188004848 A>T), RS1000238244 (4:188000441 G>A), RS1000619195 (4:187995288 C>A,G,T), RS1000678515 (4:188000692 A>G), RS10008065 (4:188005444 C>A), RS1000860872 (4:188000244 G>A,C,T), RS1000962575 (4:187994789 A>C,G), RS1001280234 (4:187999445 T>G), RS1001393699 (4:188004797 A>G), RS1001626346 (4:187994004 T>C), RS1001648080 (4:187999158 G>C,T), RS1001687771 (4:188003692 C>T), RS1001705444 (4:187993780 T>C), RS1002238879 (4:187997902 G>A), RS1002270051 (4:187998131 G>C)

Disease associations

OMIM: gene MIM:614572 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004635_11Testicular germ cell tumor2.000000e-12
GCST004713_3Testicular germ cell tumor3.000000e-08
GCST004780_10Cortisol levels (saliva)8.000000e-06
GCST008473_9Visceral fat2.000000e-06
GCST012319_12LDL levels x SSRI levels (escitalopram or citalopram) interaction in schizophrenia or bipolar disorder6.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005843cortisol measurement
EFO:0004611low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression6
methylmercuric chloridedecreases expression, increases expression3
trichostatin Aaffects cotreatment, increases expression3
sodium arseniteincreases expression2
entinostatincreases expression, affects cotreatment2
belinostatincreases expression, affects cotreatment2
Vorinostataffects cotreatment, increases expression2
Panobinostataffects cotreatment, increases expression2
Benzo(a)pyreneincreases mutagenesis, affects methylation, increases methylation2
arsenitedecreases expression, increases methylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrineincreases expression1
dorsomorphinincreases expression, affects cotreatment1
(+)-JQ1 compounddecreases expression1
Acetaminophenincreases expression1
Indomethacinincreases expression1
Malathiondecreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoindecreases expression1
Asbestos, Serpentinedecreases methylation1
Antirheumatic Agentsdecreases 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): testicular germ cell tumor