REXO4

gene
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Also known as hPMC2

Summary

REXO4 (RNA exonuclease 4, HGNC:12820) is a protein-coding gene on chromosome 9q34.2, encoding RNA exonuclease 4 (Q9GZR2).

Enables DNA binding activity and nuclease activity. Involved in DNA catabolic process and DNA repair. Located in nuclear speck and nucleolus.

Source: NCBI Gene 57109 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_020385

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12820
Approved symbolREXO4
NameRNA exonuclease 4
Location9q34.2
Locus typegene with protein product
StatusApproved
AliaseshPMC2
Ensembl geneENSG00000148300
Ensembl biotypeprotein_coding
OMIM602930
Entrez57109

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000371935, ENST00000371942, ENST00000445916, ENST00000454825, ENST00000478037, ENST00000494045, ENST00000903990, ENST00000903991, ENST00000903992, ENST00000903993, ENST00000903994

RefSeq mRNA: 4 — MANE Select: NM_020385 NM_001279349, NM_001279350, NM_001279351, NM_020385

CCDS: CCDS65179, CCDS6969

Canonical transcript exons

ENST00000371942 — 8 exons

ExonStartEnd
ENSE00000984212133410985133411073
ENSE00000984213133408768133408842
ENSE00000984214133407807133407881
ENSE00001135646133417620133418010
ENSE00003510965133412778133412921
ENSE00003532257133406062133407072
ENSE00003591439133414665133415011
ENSE00003670061133412299133412492

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2033 / max 156.6170, expressed in 1814 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
10299711.64841787
1029987.65431753
1029990.9007548

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548891.96gold quality
skeletal muscle tissueUBERON:000113490.47gold quality
gastrocnemiusUBERON:000138890.09gold quality
muscle of legUBERON:000138389.97gold quality
hindlimb stylopod muscleUBERON:000425289.24gold quality
mucosa of transverse colonUBERON:000499188.33gold quality
ventricular zoneUBERON:000305388.32gold quality
muscle tissueUBERON:000238588.00gold quality
granulocyteCL:000009487.01gold quality
cortical plateUBERON:000534386.92gold quality
ganglionic eminenceUBERON:000402386.44gold quality
apex of heartUBERON:000209886.18gold quality
body of pancreasUBERON:000115085.76gold quality
placentaUBERON:000198785.48gold quality
lymph nodeUBERON:000002985.27gold quality
prefrontal cortexUBERON:000045185.20gold quality
lower esophagus mucosaUBERON:003583485.19gold quality
calcaneal tendonUBERON:000370185.14gold quality
pancreasUBERON:000126485.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.04gold quality
right lobe of liverUBERON:000111484.93gold quality
frontal cortexUBERON:000187084.67gold quality
ovaryUBERON:000099284.63gold quality
left ovaryUBERON:000211984.59gold quality
esophagus mucosaUBERON:000246984.54gold quality
spleenUBERON:000210684.53gold quality
C1 segment of cervical spinal cordUBERON:000646984.51gold quality
stromal cell of endometriumCL:000225584.44gold quality
heart left ventricleUBERON:000208484.27gold quality
right frontal lobeUBERON:000281084.10gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no1.63

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

23 targeting REXO4, 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-12118100.0065.881270
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-426799.9666.532368
HSA-MIR-317599.6566.302031
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-766-3P99.4765.241811
HSA-MIR-20A-3P99.4469.101575
HSA-MIR-32-3P99.3668.202517
HSA-MIR-429199.2068.882969
HSA-MIR-4717-3P99.0666.341072
HSA-MIR-92299.0267.231838
HSA-MIR-4700-5P98.6367.431915
HSA-MIR-6834-3P98.1665.77551
HSA-MIR-146B-3P97.8365.29782
HSA-MIR-808997.7466.211698
HSA-MIR-4667-5P97.6166.671683
HSA-MIR-939-5P97.1065.801579
HSA-MIR-191397.0766.201417
HSA-MIR-1343-5P96.4866.061506
HSA-MIR-365195.6264.67287
HSA-MIR-4485-3P93.2162.1161

Literature-anchored findings (GeneRIF, showing 1)

  • determined that the catalytic activity of hPMC2 is required for repair of abasic sites that result from estrogen-induced DNA damage (PMID:21602889)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorexo4ENSDARG00000088619
mus_musculusRexo4ENSMUSG00000052406
rattus_norvegicusRexo4ENSRNOG00000027867
drosophila_melanogasterCG6833FBGN0036405

Paralogs (5): REXO5 (ENSG00000005189), REXO1 (ENSG00000079313), ISG20L2 (ENSG00000143319), ISG20 (ENSG00000172183), AEN (ENSG00000181026)

Protein

Protein identifiers

RNA exonuclease 4Q9GZR2 (reviewed: Q9GZR2)

Alternative names: Exonuclease XPMC2, Prevents mitotic catastrophe 2 protein homolog

All UniProt accessions (3): Q9GZR2, A0A0C4DG22, A0A0C4DG31

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Can bind ESR1 and ESR2. This interaction is abrogated by estrogen and augmented by tamoxifen treatment.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the REXO4 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9GZR2-11yes
Q9GZR2-22

RefSeq proteins (4): NP_001266278, NP_001266279, NP_001266280, NP_065118* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012337RNaseH-like_sfHomologous_superfamily
IPR013520Ribonucl_HDomain
IPR036397RNaseH_sfHomologous_superfamily
IPR037431REX4_DEDDh_domDomain
IPR047021REXO1/3/4-likeFamily

Pfam: PF00929

UniProt features (15 total): compositionally biased region 3, modified residue 3, splice variant 2, sequence variant 2, chain 1, domain 1, sequence conflict 1, region of interest 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9GZR2-F171.200.41

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 (4): 15, 96, 111, 115

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 158 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_DNA_CATABOLIC_PROCESS, CEBP_Q2, BRN2_01, PETRETTO_HEART_MASS_QTL_CIS_DN, GOBP_DNA_DAMAGE_RESPONSE, LIAO_METASTASIS, GOMF_EXONUCLEASE_ACTIVITY, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, TTCNRGNNNNTTC_HSF_Q6, GOMF_SINGLE_STRANDED_DNA_BINDING

GO Biological Process (6): DNA repair (GO:0006281), DNA catabolic process (GO:0006308), regulation of DNA-templated transcription (GO:0006355), rRNA processing (GO:0006364), RNA processing (GO:0006396), DNA metabolic process (GO:0006259)

GO Molecular Function (10): double-stranded DNA binding (GO:0003690), single-stranded DNA binding (GO:0003697), RNA binding (GO:0003723), endonuclease activity (GO:0004519), exonuclease activity (GO:0004527), 3’-5’ exonuclease activity (GO:0008408), nucleic acid binding (GO:0003676), nuclease activity (GO:0004518), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA metabolic process2
DNA binding2
nuclease activity2
binding2
nuclear lumen2
DNA damage response1
DNA nuclease activity1
nucleic acid catabolic process1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
gene expression1
RNA biosynthetic process1
primary metabolic process1
nucleic acid metabolic process1
nucleic acid binding1
hydrolase activity, acting on ester bonds1
exonuclease activity1
catalytic activity, acting on a nucleic acid1
catalytic activity1
intracellular membrane-bounded organelle1
cellular anatomical structure1
intracellular membraneless organelle1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

1988 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
REXO4REXO2Q9Y3B8827
REXO4CALCOCO2Q13137756
REXO4SP100P23497567
REXO4DEDDO75618527
REXO4CHRAC1Q9NRG0463
REXO4PWP1Q13610456
REXO4SNF8Q96H20445
REXO4KLHL36Q8N4N3403
REXO4SUPT3HO75486398
REXO4PDCD11Q14690389
REXO4ESR1P03372380
REXO4RBM11P57052371
REXO4EBPLQ9BY08367
REXO4HCCSP53701367
REXO4RASGEF1CQ8N431362

IntAct

208 interactions, top by confidence:

ABTypeScore
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
RPL14RRP8psi-mi:“MI:0914”(association)0.640
H1-1RRP8psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
RBM34RRP8psi-mi:“MI:0914”(association)0.640
RPL7ANOP56psi-mi:“MI:0914”(association)0.640
NPM1NVLpsi-mi:“MI:0914”(association)0.610
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
HSF2BPREXO4psi-mi:“MI:0915”(physical association)0.560
REXO4DNM2psi-mi:“MI:0915”(physical association)0.560
NOS3REXO4psi-mi:“MI:0915”(physical association)0.560
HTTREXO4psi-mi:“MI:0915”(physical association)0.560
ZNF512ZNF724psi-mi:“MI:0914”(association)0.530
RBM34NVLpsi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
RPL8RRP8psi-mi:“MI:0914”(association)0.530

BioGRID (332): REXO4 (Affinity Capture-RNA), REXO4 (Affinity Capture-RNA), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Co-fractionation), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS), REXO4 (Affinity Capture-MS)

ESM2 similar proteins: A3BT52, A6NIR3, A6QUM7, B5X564, F4HZF0, F4I114, F4ICB6, F4J394, O49289, P0CQ44, P0CQ45, P34442, Q09719, Q24617, Q38740, Q4IEV5, Q4PER6, Q4WHF8, Q61CX7, Q63553, Q6CE69, Q6CFE7, Q6CMT3, Q6DEW6, Q6P158, Q6P5D3, Q6PAQ4, Q753D9, Q757I9, Q7S9B7, Q8BRB7, Q8HXN7, Q8T3G2, Q8UVR5, Q8VDU5, Q8W1Y3, Q8WML3, Q8WYB5, Q91560, Q92794

Diamond homologs: A1A5R7, A1Z7K9, A3KPE8, A3LRV8, A4RF51, A5DAD0, A5E1W0, B2GUW6, G0SAK8, O94375, O94443, P0C581, P0CQ08, P0CQ09, P0CQ44, P0CQ45, P48778, P53010, P53015, P53331, Q08237, Q09798, Q0CJU7, Q10124, Q2GSV2, Q2T9U5, Q2YDK1, Q3U1G5, Q4PER6, Q4R9F7, Q4WYA1, Q504Q3, Q54U94, Q5AL29, Q5APK0, Q5B367, Q5F450, Q5REE2, Q6AXU3, Q6C462

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 170 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Peptide chain elongation2327.8×1e-25
Viral mRNA Translation2327.8×1e-25
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA2327.5×1e-25
Selenocysteine synthesis2326.3×3e-25
Eukaryotic Translation Termination2326.3×3e-25
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)2325.8×4e-25
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA2325.8×4e-25
Formation of a pool of free 40S subunits2324.5×1e-24

GO biological processes:

GO termPartnersFoldFDR
negative regulation of DNA recombination536.2×3e-05
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)530.2×6e-05
cytoplasmic translation2428.7×7e-26
chromosome condensation527.2×1e-04
ribosomal small subunit biogenesis1420.6×1e-12
ribosomal large subunit biogenesis617.2×1e-04
translation2415.9×1e-19
rRNA processing1614.6×3e-12

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance42
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1427 predictions. Top by Δscore:

VariantEffectΔscore
9:133407805:A:ACdonor_gain1.0000
9:133407806:C:CAdonor_gain1.0000
9:133407806:CTGA:Cdonor_gain1.0000
9:133407806:CTGAA:Cdonor_gain1.0000
9:133407878:CACT:Cacceptor_gain1.0000
9:133407880:CT:Cacceptor_gain1.0000
9:133407882:C:CCacceptor_gain1.0000
9:133408764:GTA:Gdonor_loss1.0000
9:133408765:TA:Tdonor_loss1.0000
9:133408766:A:Cdonor_loss1.0000
9:133408775:TG:Tdonor_gain1.0000
9:133408839:GTAC:Gacceptor_gain1.0000
9:133408840:TAC:Tacceptor_gain1.0000
9:133408841:ACCTA:Aacceptor_loss1.0000
9:133408842:CCTAG:Cacceptor_loss1.0000
9:133408843:C:CCacceptor_gain1.0000
9:133408843:CTAG:Cacceptor_loss1.0000
9:133410981:GTA:Gdonor_loss1.0000
9:133410982:TACCT:Tdonor_loss1.0000
9:133410984:C:Adonor_loss1.0000
9:133411069:TTCTC:Tacceptor_gain1.0000
9:133411071:CTC:Cacceptor_gain1.0000
9:133411072:TC:Tacceptor_gain1.0000
9:133411073:CC:Cacceptor_gain1.0000
9:133411073:CCTG:Cacceptor_loss1.0000
9:133411074:C:CCacceptor_gain1.0000
9:133411075:T:Aacceptor_loss1.0000
9:133412297:AC:Adonor_gain1.0000
9:133412298:CC:Cdonor_gain1.0000
9:133412298:CCCTG:Cdonor_gain1.0000

AlphaMissense

2779 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:133412340:C:GR290T0.994
9:133412402:G:CN269K0.994
9:133412402:G:TN269K0.994
9:133408808:C:GR345P0.993
9:133411006:G:CH326Q0.992
9:133411006:G:TH326Q0.992
9:133411010:C:TG325E0.992
9:133412339:C:AR290S0.992
9:133412339:C:GR290S0.992
9:133412340:C:AR290M0.992
9:133412413:A:GS266P0.992
9:133412418:C:GR264P0.992
9:133412421:G:TA263D0.992
9:133412468:G:CD247E0.992
9:133412468:G:TD247E0.992
9:133407019:C:AW401C0.991
9:133407019:C:GW401C0.991
9:133407065:T:GD386A0.991
9:133408806:C:GD346H0.991
9:133412327:A:CS294R0.991
9:133412327:A:TS294R0.991
9:133412329:T:GS294R0.991
9:133412370:A:TV280D0.991
9:133412475:G:TA245D0.991
9:133407021:A:GW401R0.990
9:133407021:A:TW401R0.990
9:133412412:G:AS266F0.990
9:133412462:C:AE249D0.990
9:133412462:C:GE249D0.990
9:133412463:T:AE249V0.990

dbSNP variants (sampled 300 via entrez): RS1000072422 (9:133414106 C>T), RS1000486126 (9:133408399 C>A), RS1000586973 (9:133415624 C>T), RS1000673228 (9:133410743 C>T), RS1000966775 (9:133419270 G>C), RS1001273143 (9:133419030 G>T), RS1001304283 (9:133408934 T>C,G), RS1001439782 (9:133409213 C>T), RS1001620347 (9:133407618 G>A), RS1002298160 (9:133414373 A>T), RS1002318542 (9:133411657 T>C), RS1002330166 (9:133417179 T>A), RS1002468217 (9:133419575 A>G,T), RS1002535539 (9:133415564 G>C), RS1002563267 (9:133419181 T>C)

Disease associations

OMIM: gene MIM:602930 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST004750_24Squamous cell lung carcinoma6.000000e-07
GCST010725_19Malaria9.000000e-11
GCST010725_31Malaria9.000000e-21
GCST010725_98Malaria1.000000e-19
GCST012516_2ABO blood group (AB vs O)6.000000e-18
GCST012517_2ABO blood group (B vs O)4.000000e-22
GCST012518_2ABO blood group (A vs O)2.000000e-17
GCST012519_2ABO blood group (AB vs non-AB)3.000000e-08
GCST012520_2ABO blood group (B vs non-B)8.000000e-09
GCST012522_2ABO blood group (O vs non-O)3.000000e-28

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0600062blood group AB
EFO:0600063blood group O
EFO:0600061blood group B
EFO:0600060blood group A

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression2
Cadmium Chlorideincreases abundance, increases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
bufotalinincreases expression1
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
deoxynivalenolincreases expression1
terbufosincreases methylation1
beta-lapachoneincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
coumarindecreases phosphorylation1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
di-n-butylphosphoric acidaffects expression1
perfluoro-n-nonanoic acidincreases expression1
abrineincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Arsenicaffects cotreatment, increases abundance, increases expression1
Cadmiumincreases abundance, increases expression1
Caffeinedecreases phosphorylation1
Cisplatinaffects cotreatment, decreases expression1
Cytarabinedecreases expression1
Fonofosincreases methylation1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Manganeseaffects cotreatment, increases abundance, increases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Parathionincreases methylation1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2DNAbcam HeLa REXO4 KOCancer cell lineFemale
CVCL_TI88HAP1 REXO4 (-) 1Cancer cell lineMale
CVCL_XS25HAP1 REXO4 (-) 2Cancer cell lineMale

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): malaria, squamous cell lung carcinoma