PRAP1

gene
On this page

Also known as UPA

Summary

PRAP1 (proline rich acidic protein 1, HGNC:23304) is a protein-coding gene on chromosome 10q26.3, encoding Proline-rich acidic protein 1 (Q96NZ9). Lipid-binding protein which promotes lipid absorption by facilitating MTTP-mediated lipid transfer (mainly triglycerides and phospholipids) and MTTP-mediated apoB lipoprotein assembly and secretion.

Predicted to enable triglyceride binding activity. Involved in DNA damage response, signal transduction by p53 class mediator; deactivation of mitotic spindle assembly checkpoint; and negative regulation of apoptotic process. Predicted to be located in endoplasmic reticulum and extracellular region.

Source: NCBI Gene 118471 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 28 total
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_145202

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23304
Approved symbolPRAP1
Nameproline rich acidic protein 1
Location10q26.3
Locus typegene with protein product
StatusApproved
AliasesUPA
Ensembl geneENSG00000165828
Ensembl biotypeprotein_coding
OMIM609776
Entrez118471

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000433452, ENST00000463201, ENST00000863040, ENST00000863041, ENST00000863042, ENST00000863043, ENST00000863044

RefSeq mRNA: 2 — MANE Select: NM_145202 NM_001145201, NM_145202

CCDS: CCDS44498, CCDS7679

Canonical transcript exons

ENST00000433452 — 5 exons

ExonStartEnd
ENSE00001185450133352247133352683
ENSE00001893257133347373133347425
ENSE00003791960133350095133350161
ENSE00003797617133352007133352140
ENSE00003800860133351381133351433

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 99.70.

FANTOM5 (CAGE): breadth broad, TPM avg 4.8619 / max 1517.2837, expressed in 230 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1077914.0799205
1077900.782095

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
duodenumUBERON:000211499.70gold quality
right lobe of liverUBERON:000111499.27gold quality
liverUBERON:000210798.95gold quality
mucosa of transverse colonUBERON:000499197.73gold quality
adult mammalian kidneyUBERON:000008295.32gold quality
small intestine Peyer’s patchUBERON:000345494.53gold quality
small intestineUBERON:000210894.09gold quality
rectumUBERON:000105289.10gold quality
transverse colonUBERON:000115787.55gold quality
kidneyUBERON:000211387.12gold quality
right testisUBERON:000453483.56gold quality
left testisUBERON:000453382.50gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.23silver quality
testisUBERON:000047381.63gold quality
tibial nerveUBERON:000132381.52gold quality
intestineUBERON:000016079.98gold quality
cortex of kidneyUBERON:000122577.16gold quality
colonUBERON:000115574.85gold quality
metanephros cortexUBERON:001053373.79gold quality
vermiform appendixUBERON:000115469.90gold quality
gall bladderUBERON:000211067.68gold quality
colonic epitheliumUBERON:000039764.83silver quality
monocyteCL:000057664.30gold quality
right uterine tubeUBERON:000130263.78gold quality
smooth muscle tissueUBERON:000113563.60gold quality
mucosa of stomachUBERON:000119963.42gold quality
leukocyteCL:000073862.41gold quality
ovaryUBERON:000099261.08gold quality
granulocyteCL:000009461.02gold quality
right ovaryUBERON:000211860.96gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-GEOD-125970yes12140.97
E-CURD-46yes8356.12
E-CURD-122yes3765.02
E-MTAB-9906yes2259.23
E-MTAB-8410yes1370.22
E-CURD-98yes917.48
E-HCAD-9yes55.94
E-ANND-3yes24.04
E-MTAB-3929no330.40
E-MTAB-6379no1.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

8 targeting PRAP1, 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-4731-5P99.8967.232537
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-193B-5P97.9165.88837
HSA-MIR-1234-3P86.7058.45109
HSA-MIR-7107-5P86.7059.28110

Literature-anchored findings (GeneRIF, showing 4)

  • Induction of PRAP1 expression by p53 in response to DNA-damaging agents contributes to cancer cell survival. (PMID:23235459)
  • PRAP1 is a protein interacting partner of MAD1 and that PRAP1 is able to down-regulate MAD1 and suppress mitotic checkpoint signalling in hepatocellular carcinoma. (PMID:24374861)
  • ATF3 and PRAP1 play important roles in cisplatin-induced DNA damage repair process. (PMID:29886035)
  • Proline-Rich Acidic Protein 1 (PRAP1) Protects the Gastrointestinal Epithelium From Irradiation-Induced Apoptosis. (PMID:32629119)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusPrap1ENSMUSG00000025467
rattus_norvegicusPrap1ENSRNOG00000018446

Protein

Protein identifiers

Proline-rich acidic protein 1Q96NZ9 (reviewed: Q96NZ9)

Alternative names: Epididymis tissue protein Li 178, Uterine-specific proline-rich acidic protein

All UniProt accessions (2): A6XND8, Q96NZ9

UniProt curated annotations — full annotation on UniProt →

Function. Lipid-binding protein which promotes lipid absorption by facilitating MTTP-mediated lipid transfer (mainly triglycerides and phospholipids) and MTTP-mediated apoB lipoprotein assembly and secretion. Protects the gastrointestinal epithelium from irradiation-induced apoptosis. May play an important role in maintaining normal growth homeostasis in epithelial cells. Involved in p53/TP53-dependent cell survival after DNA damage. May down-regulate the expression of MAD1L1 and exert a suppressive role in mitotic spindle assembly checkpoint in hepatocellular carcinomas.

Subunit / interactions. Interacts with isoform 1 and isoform 3 of MAD1L1. Interacts with MTTP.

Subcellular location. Secreted. Endoplasmic reticulum.

Tissue specificity. Highly expressed in the intestinal epithelial cells (at protein level). Abundantly expressed in the epithelial cells of the liver, kidney and cervix. Significantly down-regulated in hepatocellular carcinoma and right colon adenocarcinoma compared with the respective adjacent normal tissues. Expressed in epididymis (at protein level).

Induction. Up-regulated by butyrate, trichostatin A and 5’-aza-2’ deoxycytidine. Induced by DNA-damaging agents in a p53/TP53-dependent manner in HepG2 liver cancer cell line and HCT116 colon cancer cell line.

Isoforms (4)

UniProt IDNamesCanonical?
Q96NZ9-11, PRAPyes
Q96NZ9-22
Q96NZ9-33, PRAPV1
Q96NZ9-44, PRAPV2

RefSeq proteins (2): NP_001138673, NP_660203* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR027922PRAPFamily

Pfam: PF15314

UniProt features (10 total): sequence variant 4, splice variant 3, signal peptide 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96NZ9-F161.730.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_DIGESTION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_NUCLEAR_DIVISION, GOBP_REGULATION_OF_CELL_CYCLE_CHECKPOINT, GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE, GOBP_CHROMOSOME_SEPARATION, GOBP_POSITIVE_REGULATION_OF_DIGESTIVE_SYSTEM_PROCESS, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_LIPID_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT

GO Biological Process (8): DNA damage response (GO:0006974), DNA damage response, signal transduction by p53 class mediator (GO:0030330), negative regulation of apoptotic process (GO:0043066), cellular response to X-ray (GO:0071481), deactivation of mitotic spindle assembly checkpoint (GO:1902426), positive regulation of intestinal lipid absorption (GO:1904731), positive regulation of triglyceride transport (GO:1905885), positive regulation of phospholipid transport (GO:2001140)

GO Molecular Function (3): triglyceride binding (GO:0017129), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (2): extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular response to stress1
signal transduction in response to DNA damage1
signal transduction by p53 class mediator1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
response to X-ray1
cellular response to ionizing radiation1
negative regulation of mitotic spindle assembly checkpoint signaling1
intestinal lipid absorption1
positive regulation of intestinal absorption1
regulation of intestinal lipid absorption1
triglyceride transport1
positive regulation of acylglycerol transport1
regulation of triglyceride transport1
phospholipid transport1
positive regulation of lipid transport1
regulation of phospholipid transport1
lipid binding1
cellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

340 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PRAP1FUOMA2VDF0480
PRAP1RPP40O75818471
PRAP1TMEM184BQ9Y519459
PRAP1LZTS3O60299457
PRAP1NPLQ9BXD5405
PRAP1S4R460S4R460402
PRAP1RPL37AP12751401
PRAP1DSC3Q14574381
PRAP1DSC2Q02487375
PRAP1HDCP19113374
PRAP1DNPH1O43598369
PRAP1CCDC185Q8N715355
PRAP1TRNP1Q6NT89335
PRAP1ZNF511Q8NB15321
PRAP1TMEM54Q969K7318

IntAct

51 interactions, top by confidence:

ABTypeScore
PRAP1SGTApsi-mi:“MI:0915”(physical association)0.720
UBQLN1PRAP1psi-mi:“MI:0915”(physical association)0.720
SGTAPRAP1psi-mi:“MI:0915”(physical association)0.720
PRAP1UBQLN1psi-mi:“MI:0915”(physical association)0.720
PRAP1UBQLN1psi-mi:“MI:0915”(physical association)0.560
ASPHPRAP1psi-mi:“MI:0915”(physical association)0.560
MEOX2PRAP1psi-mi:“MI:0915”(physical association)0.560
PRAP1MRFAP1psi-mi:“MI:0915”(physical association)0.560
PRAP1UBQLN2psi-mi:“MI:0915”(physical association)0.560
SGTBPRAP1psi-mi:“MI:0915”(physical association)0.560
CEP19PRAP1psi-mi:“MI:0915”(physical association)0.560
HSPA6PRAP1psi-mi:“MI:0915”(physical association)0.560
AHNAK2PRAP1psi-mi:“MI:0915”(physical association)0.560
PRAP1CD48psi-mi:“MI:0914”(association)0.530
PRAP1HSPA5psi-mi:“MI:0915”(physical association)0.400
MEP1BPRAP1psi-mi:“MI:0915”(physical association)0.370
PRAP1IGHA1psi-mi:“MI:0914”(association)0.350
GRB2PRAP1psi-mi:“MI:0915”(physical association)0.000
PRAP1UBQLN2psi-mi:“MI:0915”(physical association)0.000

BioGRID (25): PRAP1 (Two-hybrid), PRAP1 (Two-hybrid), LACRT (Affinity Capture-MS), CD48 (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), UBQLN1 (Two-hybrid), CD48 (Affinity Capture-MS), LACRT (Affinity Capture-MS), LTF (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), PRAP1 (Two-hybrid), PRAP1 (Two-hybrid), PRAP1 (Two-hybrid), HSPA6 (Two-hybrid), CEP19 (Two-hybrid)

ESM2 similar proteins: A0JPP4, A2VE23, A4FU49, A8MXV6, E9Q7D5, F1NSM7, P06484, P0C671, P0C7A2, P10636, P10637, P69280, P69282, P69284, P69287, Q0VC16, Q12774, Q196W1, Q1XI13, Q28139, Q2TA21, Q4R729, Q5SRN2, Q5STT6, Q5SWP3, Q5YCV9, Q5YCW1, Q62840, Q63003, Q66666, Q66H38, Q6MG22, Q6UXA7, Q6UXF1, Q71M36, Q8BHE4, Q8BM15, Q8K4L6, Q8N1P7, Q96KW9

Diamond homologs: Q80XD8, Q96NZ9, Q9ES75

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

516 predictions. Top by Δscore:

VariantEffectΔscore
10:133352238:T:TAacceptor_gain1.0000
10:133352245:A:AGacceptor_gain1.0000
10:133352245:A:Tacceptor_loss1.0000
10:133352245:AG:Aacceptor_gain1.0000
10:133352246:G:GAacceptor_gain1.0000
10:133352246:GG:Gacceptor_gain1.0000
10:133352246:GGC:Gacceptor_gain1.0000
10:133352246:GGCA:Gacceptor_gain1.0000
10:133350090:CTCA:Cacceptor_loss0.9900
10:133350092:CA:Cacceptor_loss0.9900
10:133350093:A:AGacceptor_gain0.9900
10:133350094:G:Aacceptor_loss0.9900
10:133350094:G:GGacceptor_gain0.9900
10:133350094:GGCTC:Gacceptor_gain0.9900
10:133350157:CCAAG:Cdonor_loss0.9900
10:133350158:CAAGG:Cdonor_loss0.9900
10:133350159:AAG:Adonor_loss0.9900
10:133350161:GGTA:Gdonor_loss0.9900
10:133350162:G:GAdonor_loss0.9900
10:133351431:GAA:Gdonor_gain0.9900
10:133351434:G:GGdonor_gain0.9900
10:133352005:AG:Aacceptor_gain0.9900
10:133352006:GG:Gacceptor_gain0.9900
10:133352234:T:TAacceptor_gain0.9900
10:133352246:GGCAC:Gacceptor_gain0.9900
10:133350093:AG:Aacceptor_gain0.9800
10:133350094:GG:Gacceptor_gain0.9800
10:133352001:CAGCA:Cacceptor_loss0.9800
10:133352004:CAGG:Cacceptor_loss0.9800
10:133352005:A:AGacceptor_gain0.9800

AlphaMissense

981 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:133352417:G:CD145H0.936
10:133352419:C:AD145E0.934
10:133352419:C:GD145E0.934
10:133352418:A:CD145A0.932
10:133350111:A:CS9R0.931
10:133350113:C:AS9R0.931
10:133350113:C:GS9R0.931
10:133352418:A:TD145V0.924
10:133352411:G:CD143H0.911
10:133352431:C:AH149Q0.907
10:133352431:C:GH149Q0.907
10:133352412:A:CD143A0.904
10:133352413:C:AD143E0.896
10:133352413:C:GD143E0.896
10:133352429:C:GH149D0.889
10:133352418:A:GD145G0.867
10:133352313:A:TD110V0.858
10:133352412:A:TD143V0.852
10:133352314:C:AD110E0.841
10:133352314:C:GD110E0.841
10:133352326:C:AH114Q0.841
10:133352326:C:GH114Q0.841
10:133352407:G:CE141D0.827
10:133352407:G:TE141D0.827
10:133352399:G:AG139R0.825
10:133352399:G:CG139R0.825
10:133352313:A:CD110A0.824
10:133352412:A:GD143G0.817
10:133352324:C:GH114D0.805
10:133352312:G:CD110H0.795

dbSNP variants (sampled 300 via entrez): RS1000394913 (10:133350536 C>A), RS1000427476 (10:133350804 C>A,G,T), RS1001157769 (10:133345542 T>A), RS1001565324 (10:133350256 T>C), RS1001932617 (10:133349897 C>T), RS1003204110 (10:133348755 T>C), RS1003644616 (10:133348968 C>T), RS1005668422 (10:133348083 C>T), RS1005829653 (10:133353139 G>A,C), RS1006088770 (10:133347112 G>A), RS1006205892 (10:133352358 G>A,C), RS1007086286 (10:133346587 G>A,C,T), RS1007423177 (10:133352126 G>A,T), RS1007482678 (10:133346602 A>G), RS1007795975 (10:133351848 C>T)

Disease associations

OMIM: gene MIM:609776 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007250_1Nonunion in individuals with fractures2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009707fractures, ununited

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4879502 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 398 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL4098253AZD24611398

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

ChEMBL bioactivities

6 potent at pChembl≥5 of 6 total, top 6 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.16IC506.87nMCHEMBL4854774
8.15IC507.09nMAZD2461
8.08IC508.35nMCHEMBL4850135
7.87IC5013.56nMCHEMBL4856941
7.82IC5015.28nMCHEMBL4869660
7.72IC5019.09nMCHEMBL4849327

PubChem BioAssay actives

6 with measured affinity, of 6 total; 6 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
3-acetamido-N-[(4,6-dimethyl-2-oxo-1H-pyridin-3-yl)methyl]-5-[6-[4-[2-fluoro-5-[(4-oxo-3H-phthalazin-1-yl)methyl]benzoyl]piperazin-1-yl]-3-pyridinyl]-2-methylbenzamide1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0069uM
4-[[4-fluoro-3-(4-methoxypiperidine-1-carbonyl)phenyl]methyl]-2H-phthalazin-1-one1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0071uM
N-[(4,6-dimethyl-2-oxo-1H-pyridin-3-yl)methyl]-5-[6-[4-[2-fluoro-5-[(4-oxo-3H-phthalazin-1-yl)methyl]benzoyl]piperazin-1-yl]-3-pyridinyl]-2-methyl-3-(propanoylamino)benzamide1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0083uM
N-[(4,6-dimethyl-2-oxo-1H-pyridin-3-yl)methyl]-3-[ethyl(propanoyl)amino]-5-[6-[4-[2-fluoro-5-[(4-oxo-3H-phthalazin-1-yl)methyl]benzoyl]piperazin-1-yl]-3-pyridinyl]-2-methylbenzamide1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0136uM
N-[(4,6-dimethyl-2-oxo-1H-pyridin-3-yl)methyl]-5-[6-[4-[2-fluoro-5-[(4-oxo-3H-phthalazin-1-yl)methyl]benzoyl]piperazin-1-yl]-3-pyridinyl]-2-methyl-3-(3-methylbutanoylamino)benzamide1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0153uM
N-[(4,6-dimethyl-2-oxo-1H-pyridin-3-yl)methyl]-3-[ethyl(2-methylprop-2-enoyl)amino]-5-[6-[4-[2-fluoro-5-[(4-oxo-3H-phthalazin-1-yl)methyl]benzoyl]piperazin-1-yl]-3-pyridinyl]-2-methylbenzamide1773629: Inhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayic500.0191uM

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression4
Aflatoxin B1affects expression, decreases expression, increases expression3
sodium arsenitedecreases expression, increases expression, decreases reaction, increases secretion2
Valproic Acidaffects expression, decreases expression2
tris(2-butoxyethyl) phosphateaffects expression1
2,4,5,2’,4’,5’-hexachlorobiphenylincreases expression1
CGP 52608affects binding, increases reaction1
bisphenol Saffects methylation, affects cotreatment, decreases methylation1
jinfukangaffects cotreatment, increases expression1
theaflavin-3,3’-digallateaffects expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Cisplatinincreases expression, affects cotreatment1
Plant Extractsaffects cotreatment, decreases expression1
Quercetinincreases expression1
Tetrachlorodibenzodioxinincreases expression1
Cyclosporinedecreases expression1
Okadaic Aciddecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4833010BindingInhibition of PRAP1 (unknown origin) by HT universal chemiluminescent assayDiscovery of First-in-Class Dual PARP and EZH2 Inhibitors for Triple-Negative Breast Cancer with Wild-Type BRCA. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2C1Abcam HeLa PRAP1 KOCancer cell lineFemale

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.