PARPBP

gene
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Also known as FLJ20641PARI

Summary

PARPBP (PARP1 binding protein, HGNC:26074) is a protein-coding gene on chromosome 12q23.2, encoding PCNA-interacting partner (Q9NWS1). Required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability.

Predicted to enable DNA binding activity. Involved in negative regulation of double-strand break repair via homologous recombination. Located in chromatin and nucleoplasm.

Source: NCBI Gene 55010 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 105 total
  • MANE Select transcript: NM_017915

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26074
Approved symbolPARPBP
NamePARP1 binding protein
Location12q23.2
Locus typegene with protein product
StatusApproved
AliasesFLJ20641, PARI
Ensembl geneENSG00000185480
Ensembl biotypeprotein_coding
OMIM613687
Entrez55010

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 19 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000327680, ENST00000392909, ENST00000392911, ENST00000392914, ENST00000412715, ENST00000417507, ENST00000457614, ENST00000535811, ENST00000537257, ENST00000541394, ENST00000541668, ENST00000543784, ENST00000852220, ENST00000852221, ENST00000852222, ENST00000852223, ENST00000929768, ENST00000929769, ENST00000929770, ENST00000929771, ENST00000929772, ENST00000929773, ENST00000967998, ENST00000967999

RefSeq mRNA: 67 — MANE Select: NM_017915 NM_001319988, NM_001319993, NM_001319994, NM_001319996, NM_001382721, NM_001382722, NM_001382723, NM_001382724, NM_001382725, NM_001382726, NM_001382728, NM_001382729, NM_001382731, NM_001382732, NM_001382735, NM_001400853, NM_001400854, NM_001400855, NM_001400856, NM_001400857, NM_001400858, NM_001400859, NM_001400860, NM_001400861, NM_001400862, NM_001400863, NM_001400864, NM_001400865, NM_001400866, NM_001400867, NM_001400868, NM_001400869, NM_001400870, NM_001400871, NM_001400872, NM_001400873, NM_001400874, NM_001400875, NM_001400876, NM_001400877, NM_001400878, NM_001400879, NM_001400880, NM_001400881, NM_001400883, NM_001400885, NM_001400886, NM_001400887, NM_001400888, NM_001400889, NM_001400890, NM_001400891, NM_001400892, NM_001400893, NM_001400894, NM_001400895, NM_001400902, NM_001400903, NM_001400905, NM_001400906, NM_001400907, NM_001400925, NM_001400926, NM_001400927, NM_001400928, NM_001400929, NM_017915

CCDS: CCDS81728, CCDS81729, CCDS81730, CCDS9090, CCDS91743

Canonical transcript exons

ENST00000327680 — 11 exons

ExonStartEnd
ENSE00001314302102164438102164608
ENSE00003490031102123886102124041
ENSE00003495299102165729102165883
ENSE00003502613102182549102182627
ENSE00003529925102175483102175666
ENSE00003571928102195951102197520
ENSE00003591981102195312102195447
ENSE00003595314102153869102153976
ENSE00003654471102178592102178770
ENSE00003747564102148230102148463
ENSE00003908586102120183102120286

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 88.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7666 / max 204.9543, expressed in 1541 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1276786.22981393
1276791.9197853
1276801.5825737
1276810.03477

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.27gold quality
ventricular zoneUBERON:000305387.50gold quality
ganglionic eminenceUBERON:000402382.66gold quality
secondary oocyteCL:000065582.39gold quality
embryoUBERON:000092281.29gold quality
lower esophagus mucosaUBERON:003583481.14gold quality
tongue squamous epitheliumUBERON:000691979.05silver quality
bone marrow cellCL:000209276.68gold quality
rectumUBERON:000105276.45gold quality
stromal cell of endometriumCL:000225576.41gold quality
adrenal tissueUBERON:001830376.27gold quality
mucosa of transverse colonUBERON:000499176.24gold quality
esophagus mucosaUBERON:000246975.82gold quality
bone marrowUBERON:000237175.35gold quality
endometriumUBERON:000129573.61gold quality
epithelium of nasopharynxUBERON:000195172.43gold quality
vermiform appendixUBERON:000115470.66gold quality
hair follicleUBERON:000207370.28gold quality
lymph nodeUBERON:000002970.01gold quality
monocyteCL:000057669.97gold quality
mononuclear cellCL:000084269.78gold quality
leukocyteCL:000073869.69gold quality
hypothalamusUBERON:000189868.88gold quality
smooth muscle tissueUBERON:000113568.79gold quality
calcaneal tendonUBERON:000370168.45gold quality
esophagusUBERON:000104368.13gold quality
testisUBERON:000047367.74gold quality
colonic epitheliumUBERON:000039767.69gold quality
right testisUBERON:000453467.55gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting PARPBP, 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-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4682100.0068.891258
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-9-5P100.0072.282361
HSA-MIR-3646100.0073.565283
HSA-MIR-1213699.9872.815713
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-806399.9169.763146
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-544A99.8468.661965
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-94499.8270.853042
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-548A-3P99.7670.583524

Literature-anchored findings (GeneRIF, showing 11)

  • Demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1). Knockdown of C12orf48 by siRNA in PDAC cells significantly suppressed their growth. (PMID:20931645)
  • PARI suppresses inappropriate recombination events at mammalian replication forks. (PMID:22153967)
  • Knockdown of C12orf48 by siRNA in HeLa cells significantly suppressed their growth (PMID:23039964)
  • PARI overexpression promotes genomic instability and pancreatic tumorigenesis. (PMID:23436799)
  • PARI inhibits homologous recombination in vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells (PMID:26792895)
  • PARI is a latent modulator of stalled fork processing, which is required for stable genome inheritance under both endogenous and exogenous replication stress (PMID:28894029)
  • PARI plays potential oncogenic roles and functions as a transcriptional target and effector of FOXM1 in gastric cancer development (PMID:29805304)
  • PARP1-binding protein was significantly upregulated in Hepatocellular Carcinoma tissues compared with normal liver. High PARPBP expression was associated with elevated serum AFP level, vascular invasion, poor tumor differentiation, and advanced TNM stage. (PMID:30949905)
  • show that PARI expression negatively correlates with expression of differentiation markers in clinical myeloid leukemia samples, suggesting that targeting PARI may restore differentiation ability of leukemia cells and antagonize their proliferation (PMID:30967629)
  • PARPBP expression is enhanced in lung adenocarcinoma tissues and is a potential factor in the progression of lung adenocarcinoma. (PMID:31611199)
  • SNORA70E promotes the occurrence and development of ovarian cancer through pseudouridylation modification of RAP1B and alternative splicing of PARPBP. (PMID:36056690)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioparpbpENSDARG00000029944
mus_musculusParpbpENSMUSG00000035365
rattus_norvegicusParpbpENSRNOG00000004682

Protein

Protein identifiers

PCNA-interacting partnerQ9NWS1 (reviewed: Q9NWS1)

Alternative names: PARP-1 binding protein, PARP1-binding protein

All UniProt accessions (7): Q9NWS1, A0A0C4DG30, B4DT40, B4DZ31, G8JLI2, H0Y6B3, J3KQY3

UniProt curated annotations — full annotation on UniProt →

Function. Required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by interfering with the formation of the RAD51-DNA homologous recombination structure. Binds single-strand DNA and poly(A) homopolymers. Positively regulate the poly(ADP-ribosyl)ation activity of PARP1; however such function may be indirect.

Subunit / interactions. Interacts with RAD51 and PCNA. Interacts with PARP1. Interacts with TASOR.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Restricted to testis. Overexpressed in multiple cancer cells.

Domain organisation. Although it shares some sequence similarity with SRS2 yeast helicase, does not contain a functional ATPase domain suggesting it has no helicase activity.

Similarity. Belongs to the PARI family.

Isoforms (7)

UniProt IDNamesCanonical?
Q9NWS1-11yes
Q9NWS1-22
Q9NWS1-33
Q9NWS1-44
Q9NWS1-55
Q9NWS1-66
Q9NWS1-77

RefSeq proteins (66): NP_001306917, NP_001306922, NP_001306923, NP_001306925, NP_001369650, NP_001369651, NP_001369652, NP_001369653, NP_001369654, NP_001369655, NP_001369657, NP_001369658, NP_001369660, NP_001369661, NP_001369664, NP_001387782, NP_001387783, NP_001387784, NP_001387785, NP_001387786, NP_001387787, NP_001387788, NP_001387789, NP_001387790, NP_001387791, NP_001387792, NP_001387793, NP_001387794, NP_001387795, NP_001387796, NP_001387797, NP_001387798, NP_001387799, NP_001387800, NP_001387801, NP_001387802, NP_001387803, NP_001387804, NP_001387805, NP_001387806, NP_001387807, NP_001387808, NP_001387809, NP_001387810, NP_001387812, NP_001387814, NP_001387815, NP_001387816, NP_001387817, NP_001387818, NP_001387819, NP_001387820, NP_001387821, NP_001387822, NP_001387823, NP_001387824, NP_001387831, NP_001387832, NP_001387835, NP_001387836, NP_001387854, NP_001387855, NP_001387856, NP_001387857, NP_001387858, NP_060385* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR027417P-loop_NTPaseHomologous_superfamily
IPR038932PARPBPFamily

UniProt features (21 total): splice variant 11, sequence conflict 6, chain 1, region of interest 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NWS1-F170.700.37

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 189 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_REGULATION_OF_DNA_RECOMBINATION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_NEGATIVE_REGULATION_OF_DNA_REPAIR, GOBP_NEGATIVE_REGULATION_OF_DNA_RECOMBINATION, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR_VIA_HOMOLOGOUS_RECOMBINATION, GOBP_REGULATION_OF_DNA_REPAIR, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_DNA_DAMAGE_RESPONSE, FUJII_YBX1_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_STRESS, FISCHER_DREAM_TARGETS, GOBP_RECOMBINATIONAL_REPAIR

GO Biological Process (3): DNA repair (GO:0006281), negative regulation of double-strand break repair via homologous recombination (GO:2000042), DNA damage response (GO:0006974)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
DNA metabolic process1
DNA damage response1
double-strand break repair via homologous recombination1
regulation of double-strand break repair via homologous recombination1
negative regulation of DNA recombination1
negative regulation of double-strand break repair1
cellular response to stress1
nucleic acid binding1
binding1
chromosome1
nuclear lumen1
intracellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

3020 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PARPBPPMCHP20382871
PARPBPPARP1P09874802
PARPBPFIRRMQ9NSG2536
PARPBPH1-0P07305520
PARPBPHSP90AB1P08238500
PARPBPHSP90AA1P07900457
PARPBPWASHC3Q9Y3C0449
PARPBPRAD54LQ92698430
PARPBPNUP37Q8NFH4427
PARPBPCENPIQ92674398
PARPBPRAD51AP1Q96B01394
PARPBPNCAPHQ15003378
PARPBPNPTX1Q15818374
PARPBPCHODLQ9H9P2373
PARPBPHGH1P0CB43371

IntAct

5 interactions, top by confidence:

ABTypeScore
PARPBPH1-2psi-mi:“MI:0915”(physical association)0.400
NEK4E2F8psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
PARPBPRPSA2psi-mi:“MI:0914”(association)0.350

BioGRID (17): PCNA (Reconstituted Complex), PCNA (Affinity Capture-Western), PARPBP (Reconstituted Complex), RAD51 (Reconstituted Complex), PARPBP (Reconstituted Complex), RAD51 (Biochemical Activity), PARPBP (Two-hybrid), PARPBP (Synthetic Lethality), PARPBP (Proximity Label-MS), PARPBP (Affinity Capture-MS), APOO (Affinity Capture-MS), RPSAP58 (Affinity Capture-MS), PCBP3 (Affinity Capture-MS), PARPBP (Affinity Capture-MS), PARPBP (Proximity Label-MS)

ESM2 similar proteins: F5H982, O36361, O36373, O36381, O36417, O36419, O36420, O42654, O74387, O75818, P09284, P0C6Z9, P0CAE8, P0CAE9, P0DTP3, P0DTP4, P24437, P26003, P29882, P38299, P40385, P52348, P52359, P52363, P52364, P52376, P52441, P52465, P52534, P92529, Q01021, Q01032, Q01041, Q01500, Q12366, Q18LE3, Q28EM3, Q567C3, Q5RA78, Q5ZKL9

Diamond homologs: F1MF21, Q1RMA6, Q28EM3, Q32N66, Q5ZKL9, Q6IRT3, Q9EQ10, Q9NWS1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance80
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2426 predictions. Top by Δscore:

VariantEffectΔscore
12:102120284:CACGT:Cdonor_loss1.0000
12:102120286:CG:Cdonor_loss1.0000
12:102120287:G:GGdonor_gain1.0000
12:102120288:TAA:Tdonor_loss1.0000
12:102123878:A:AGacceptor_gain1.0000
12:102123879:C:Gacceptor_gain1.0000
12:102123881:TTAA:Tacceptor_loss1.0000
12:102123882:TAAG:Tacceptor_loss1.0000
12:102123883:A:AGacceptor_gain1.0000
12:102123884:A:Cacceptor_loss1.0000
12:102123884:A:Gacceptor_gain1.0000
12:102123885:G:Aacceptor_loss1.0000
12:102123885:G:GGacceptor_gain1.0000
12:102123885:GATA:Gacceptor_gain1.0000
12:102124040:AG:Adonor_loss1.0000
12:102124041:GGT:Gdonor_loss1.0000
12:102124042:G:GCdonor_loss1.0000
12:102148344:G:GTdonor_gain1.0000
12:102148352:G:GTdonor_gain1.0000
12:102148376:GAACA:Gdonor_gain1.0000
12:102148380:A:AGdonor_gain1.0000
12:102148381:G:GGdonor_gain1.0000
12:102148384:A:AGdonor_gain1.0000
12:102178590:A:AGacceptor_gain1.0000
12:102178591:G:GGacceptor_gain1.0000
12:102195944:A:AGacceptor_gain1.0000
12:102195945:T:Gacceptor_gain1.0000
12:102195949:A:AGacceptor_gain1.0000
12:102195949:AGAG:Aacceptor_gain1.0000
12:102195950:G:GGacceptor_gain1.0000

AlphaMissense

3844 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:102148242:T:CF56L0.989
12:102148244:T:AF56L0.989
12:102148244:T:GF56L0.989
12:102195339:T:CF431L0.987
12:102195341:T:AF431L0.987
12:102195341:T:GF431L0.987
12:102124024:G:CA46P0.985
12:102164558:T:CF206L0.983
12:102164560:C:AF206L0.983
12:102164560:C:GF206L0.983
12:102124016:T:CL43P0.981
12:102123938:G:CR17P0.979
12:102148275:T:AW67R0.978
12:102148275:T:CW67R0.978
12:102165741:T:CF227L0.976
12:102165743:T:AF227L0.976
12:102165743:T:GF227L0.976
12:102164491:T:AN183K0.974
12:102164491:T:GN183K0.974
12:102164572:A:CK210N0.973
12:102164572:A:TK210N0.973
12:102164579:G:CA213P0.973
12:102196277:T:CF576L0.970
12:102196279:T:AF576L0.970
12:102196279:T:GF576L0.970
12:102164559:T:CF206S0.969
12:102164568:T:CL209S0.968
12:102165733:C:AA224D0.968
12:102165820:T:CL253S0.967
12:102153876:T:CL132P0.966

dbSNP variants (sampled 300 via entrez): RS1000003553 (12:102144365 G>A), RS1000033222 (12:102185716 T>C), RS1000056660 (12:102189414 C>T), RS1000169838 (12:102130211 C>T), RS1000226041 (12:102172526 T>C), RS1000254806 (12:102195858 C>A,T), RS1000257514 (12:102139172 G>GT), RS1000264422 (12:102122230 T>C), RS1000390572 (12:102192376 C>T), RS1000410149 (12:102165594 G>A), RS1000439664 (12:102144700 C>G), RS1000461623 (12:102179564 C>T), RS1000521475 (12:102181853 T>C), RS1000555509 (12:102176605 T>C), RS1000564923 (12:102173953 T>C)

Disease associations

OMIM: gene MIM:613687 | 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
GCST000522_7Height8.000000e-06
GCST004863_37Mosquito bite size1.000000e-06
GCST008839_173Height3.000000e-97
GCST010002_221Refractive error3.000000e-10
GCST010703_2Brain morphology (MOSTest)3.000000e-37
GCST012228_552Waist-hip index2.000000e-08
GCST012230_46Waist-to-hip ratio adjusted for BMI7.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0008378mosquito bite reaction size measurement
EFO:0004346neuroimaging measurement
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs11111201PARPBP, PMCH0.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Cyclosporinedecreases expression3
bisphenol Adecreases expression2
Valproic Aciddecreases expression2
aristolochic acid Idecreases expression1
afuresertibdecreases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chlorideincreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
diallyl trisulfidedecreases expression1
2-palmitoylglycerolincreases expression1
bisphenol Sdecreases expression, affects cotreatment1
incobotulinumtoxinAdecreases expression1
Dasatinibdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Vorinostatincreases expression1
Acetaminophenincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Azathioprinedecreases expression1
Benzo(a)pyrenedecreases expression1
Calcitrioldecreases expression, affects cotreatment1
Coumestrolaffects cotreatment, increases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Folic Aciddecreases expression, affects cotreatment1
Formaldehydedecreases expression1
Hydrogen Peroxideaffects expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_TC26HAP1 PARPBP (-) 1Cancer cell lineMale
CVCL_TC27HAP1 PARPBP (-) 2Cancer cell lineMale

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.