RPE

gene
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Summary

RPE (ribulose-5-phosphate-3-epimerase, HGNC:10293) is a protein-coding gene on chromosome 2q34, encoding Ribulose-phosphate 3-epimerase (Q96AT9). Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate. It is a selective cancer dependency (DepMap: 77.1% of cell lines).

Enables D-ribulose-phosphate 3-epimerase activity; metal ion binding activity; and protein homodimerization activity. Involved in carbohydrate metabolic process and pentose-phosphate shunt. Located in extracellular exosome.

Source: NCBI Gene 6120 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 27 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 77.1% of screened cell lines
  • MANE Select transcript: NM_199229

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10293
Approved symbolRPE
Nameribulose-5-phosphate-3-epimerase
Location2q34
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000197713
Ensembl biotypeprotein_coding
OMIM180480
Entrez6120

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 19 protein_coding, 1 nonsense_mediated_decay

ENST00000354506, ENST00000359429, ENST00000408981, ENST00000411934, ENST00000429907, ENST00000429921, ENST00000435437, ENST00000436630, ENST00000438191, ENST00000438204, ENST00000438265, ENST00000441588, ENST00000445268, ENST00000452025, ENST00000453724, ENST00000454822, ENST00000867610, ENST00000867611, ENST00000924218, ENST00000924219

RefSeq mRNA: 14 — MANE Select: NM_199229 NM_001278282, NM_001278283, NM_001278285, NM_001278286, NM_001278288, NM_001278289, NM_001318926, NM_001318927, NM_001318928, NM_001318929, NM_001318930, NM_001318931, NM_006916, NM_199229

CCDS: CCDS2388, CCDS42810, CCDS63107, CCDS63108, CCDS82567, CCDS82568

Canonical transcript exons

ENST00000359429 — 6 exons

ExonStartEnd
ENSE00001582404210016507210016641
ENSE00001583054210017473210017559
ENSE00003528033210009657210009736
ENSE00003674772210015973210016112
ENSE00003843678210019669210022260
ENSE00003848802210002638210002783

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 95.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.1881 / max 620.4743, expressed in 1812 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
2500321.57331805
250023.61481579

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830395.68gold quality
islet of LangerhansUBERON:000000692.69gold quality
calcaneal tendonUBERON:000370192.32gold quality
colonic epitheliumUBERON:000039791.87gold quality
rectumUBERON:000105291.74gold quality
bone marrow cellCL:000209291.36gold quality
Brodmann (1909) area 23UBERON:001355491.33gold quality
esophagus squamous epitheliumUBERON:000692090.98gold quality
endothelial cellCL:000011590.70gold quality
epithelium of esophagusUBERON:000197690.25gold quality
ventricular zoneUBERON:000305390.20gold quality
stromal cell of endometriumCL:000225590.12gold quality
endometriumUBERON:000129589.29gold quality
right adrenal gland cortexUBERON:003582789.20gold quality
right adrenal glandUBERON:000123389.10gold quality
gingival epitheliumUBERON:000194989.09gold quality
monocyteCL:000057689.04gold quality
cortical plateUBERON:000534388.88gold quality
mononuclear cellCL:000084288.87gold quality
adrenal glandUBERON:000236988.78gold quality
medial globus pallidusUBERON:000247788.71gold quality
germinal epithelium of ovaryUBERON:000130488.70gold quality
gall bladderUBERON:000211088.70gold quality
smooth muscle tissueUBERON:000113588.69gold quality
tonsilUBERON:000237288.68gold quality
leukocyteCL:000073888.60gold quality
oocyteCL:000002388.57gold quality
left adrenal glandUBERON:000123488.56gold quality
secondary oocyteCL:000065588.54gold quality
prefrontal cortexUBERON:000045188.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting RPE, 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-3163100.0077.238605
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-60799.9773.625593
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-570-3P99.9672.414910
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-806399.9169.763146
HSA-MIR-329-3P99.9166.561234
HSA-MIR-362-3P99.9166.381267
HSA-MIR-652-5P99.9167.49505
HSA-MIR-367199.9073.043897
HSA-MIR-95-5P99.8972.173973
HSA-MIR-153-5P99.8973.866317
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • The binary complexes of RPE reported here will aid in the design of small molecules for modulating the activity of the enzyme and altering flux through the pentose phosphate pathway. (PMID:20923965)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorpeENSDARG00000005251
mus_musculusRpeENSMUSG00000026005
rattus_norvegicusRpeENSRNOG00000038085
drosophila_melanogasterRpeFBGN0050499
caenorhabditis_elegansWBGENE00017272

Paralogs (1): RPEL1 (ENSG00000235376)

Protein

Protein identifiers

Ribulose-phosphate 3-epimeraseQ96AT9 (reviewed: Q96AT9)

Alternative names: Ribulose-5-phosphate-3-epimerase

All UniProt accessions (10): C9IYE8, C9IZU8, C9J6A7, C9J8S0, C9J9T0, C9JCL8, E7ESZ6, E9PBG9, Q96AT9, F8WBT4

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.

Subunit / interactions. Homodimer.

Cofactor. Binds 1 divalent metal cation per subunit. Active with Fe(2+), and probably also with Mn(2+), Zn(2+) and Co(2+).

Pathway. Carbohydrate degradation.

Similarity. Belongs to the ribulose-phosphate 3-epimerase family.

Isoforms (5)

UniProt IDNamesCanonical?
Q96AT9-11yes
Q96AT9-22
Q96AT9-33
Q96AT9-44
Q96AT9-55

RefSeq proteins (14): NP_001265211, NP_001265212, NP_001265214, NP_001265215, NP_001265217, NP_001265218, NP_001305855, NP_001305856, NP_001305857, NP_001305858, NP_001305859, NP_001305860, NP_008847, NP_954699* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000056Ribul_P_3_epim-likeFamily
IPR011060RibuloseP-bd_barrelHomologous_superfamily
IPR013785Aldolase_TIMHomologous_superfamily
IPR026019Ribul_P_3_epimFamily

Pfam: PF00834

Enzyme classification (BRENDA):

  • EC 5.1.3.1 — ribulose-phosphate 3-epimerase (BRENDA: 21 organisms, 16 substrates, 17 inhibitors, 16 Km, 13 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
D-RIBULOSE 5-PHOSPHATE0.056–1513
D-RIBULOSE-5-PHOSPHATE2.4–2.92
D-XYLULOSE 5-PHOSPHATE0

Catalyzed reactions (Rhea), 1 shown:

  • D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)

UniProt features (53 total): helix 14, binding site 9, mutagenesis site 9, strand 9, splice variant 4, active site 2, turn 2, initiator methionine 1, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
3OVPX-RAY DIFFRACTION1.7
3OVRX-RAY DIFFRACTION1.95
3OVQX-RAY DIFFRACTION2
3QC3X-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96AT9-F196.610.96

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 37 (proton acceptor); 175 (proton donor)

Ligand- & substrate-binding residues (9): 175–177; 175; 197–198; 10; 35; 37; 70; 70; 146–149

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (9):

PositionPhenotype
10nearly abolishes enzyme activity.
12reduces enzyme activity by half.
35alters protein structure. nearly abolishes enzyme activity.
37alters protein structure. nearly abolishes enzyme activity.
39lowers enzyme activity by 10%.
70alters protein structure.
72reduces enzyme activity by half.
141no effect on enzyme activity.
175alters protein structure.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-71336Pentose phosphate pathway
R-HSA-1430728Metabolism
R-HSA-71387Metabolism of carbohydrates and carbohydrate derivatives

MSigDB gene sets: 179 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, BROWNE_HCMV_INFECTION_6HR_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_NADPPLUS_METABOLIC_PROCESS, MODULE_151, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_GLUCOSE_6_PHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY

GO Biological Process (3): carbohydrate metabolic process (GO:0005975), pentose-phosphate shunt (GO:0006098), pentose-phosphate shunt, non-oxidative branch (GO:0009052)

GO Molecular Function (7): D-ribulose-phosphate 3-epimerase activity (GO:0004750), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), metal ion binding (GO:0046872), protein binding (GO:0005515), isomerase activity (GO:0016853), racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)

GO Cellular Component (2): cytosol (GO:0005829), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Metabolism of carbohydrates and carbohydrate derivatives1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
primary metabolic process1
NADPH regeneration1
pentose-phosphate shunt, oxidative branch1
pentose-phosphate shunt, non-oxidative branch1
glucose 6-phosphate metabolic process1
D-ribulose-phosphate 3-epimerase activity1
ribose-5-phosphate isomerase activity1
transaldolase activity1
transketolase activity1
generation of precursor metabolites and energy1
pentose-phosphate shunt1
glyceraldehyde-3-phosphate metabolic process1
racemase and epimerase activity, acting on carbohydrates and derivatives1
protein binding1
identical protein binding1
protein dimerization activity1
cation binding1
binding1
catalytic activity1
racemase and epimerase activity1
cytoplasm1
cellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

2124 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPERPIAP49247895
RPETALDO1P37837837
RPETKTP29401822
RPETKTL1P51854776
RPETKTL2Q9H0I9760
RPEGPIP06744760
RPETPI1P00938743
RPEPGDP52209738
RPEH6PDO95479725
RPEXYLBO75191718
RPEPGLSO95336686
RPEG6PDP11413630
RPEFHP07954618
RPEPGK2P07205608
RPERBKSQ9H477600
RPECSO75390600

IntAct

19 interactions, top by confidence:

ABTypeScore
RPERPEpsi-mi:“MI:0915”(physical association)0.810
RPERPEpsi-mi:“MI:0407”(direct interaction)0.810
GCD7RPEpsi-mi:“MI:0915”(physical association)0.560
RPEGCD7psi-mi:“MI:0915”(physical association)0.560
RPEPLEKHF2psi-mi:“MI:0915”(physical association)0.560
RPEGPX4psi-mi:“MI:0915”(physical association)0.400
PRNPCARNS1psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
RPEAPODpsi-mi:“MI:0914”(association)0.350
RPERPEpsi-mi:“MI:0915”(physical association)0.000
PLEKHF2RPEpsi-mi:“MI:0915”(physical association)0.000
RPEserB2psi-mi:“MI:0915”(physical association)0.000
EXOSC10RPEpsi-mi:“MI:0915”(physical association)0.000

BioGRID (68): RPE (Two-hybrid), CLU (Affinity Capture-MS), APOD (Affinity Capture-MS), RPE (Two-hybrid), ADSL (Co-fractionation), ALDH2 (Co-fractionation), ALDH5A1 (Co-fractionation), ALDOB (Co-fractionation), IDE (Co-fractionation), IMPA2 (Co-fractionation), MAP2K1 (Co-fractionation), MAP2K2 (Co-fractionation), NRBP1 (Co-fractionation), NUTF2 (Co-fractionation), PGK2 (Co-fractionation)

ESM2 similar proteins: A0A2P6MHY1, A7ZAH2, A8AQ28, A8B2U2, A9MPP7, B0B7Q0, B1LFP2, B7NDC5, B7UJ37, O14105, O34557, O67098, O84123, P07601, P0AG07, P0AG08, P0AG09, P0AG10, P0CE21, P32719, P42420, P44756, P45455, P46969, P56109, P56188, P57603, P74061, P77704, Q1QMP2, Q2QD12, Q3AR00, Q3MEN8, Q3SRG9, Q58093, Q5R5Y2, Q5WKY5, Q6FL81, Q755M2, Q8K940

Diamond homologs: O14105, O34557, O66107, O67098, O84123, P0AG07, P0AG08, P0AG09, P0AG10, P32719, P39362, P40117, P44756, P45455, P46969, P47358, P51012, P51013, P56188, P57603, P65761, P74061, P75522, P9WI50, P9WI51, Q04539, Q2QD12, Q43157, Q43843, Q58093, Q5R5Y2, Q6FL81, Q755M2, Q89A59, Q8K940, Q8SRP6, Q8VEE0, Q96AT9, Q9CCP9, Q9L0Z5

SIGNOR signaling

2 interactions.

AEffectBMechanism
RPE“down-regulates quantity”“D-ribulose 5-phosphate”“chemical modification”
RPE“up-regulates quantity”“D-xylulose 5-phosphate(2-)”“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance15
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
979400GRCh37/hg19 2q33.2-34(chr2:204445619-212580788)x1Pathogenic

SpliceAI

1508 predictions. Top by Δscore:

VariantEffectΔscore
2:210002770:G:GTdonor_gain1.0000
2:210014610:G:GGdonor_gain1.0000
2:210015968:TCTA:Tacceptor_loss1.0000
2:210015971:A:AGacceptor_gain1.0000
2:210015971:A:Tacceptor_loss1.0000
2:210015972:G:GTacceptor_gain1.0000
2:210015972:GA:Gacceptor_gain1.0000
2:210015972:GAC:Gacceptor_gain1.0000
2:210015972:GACA:Gacceptor_gain1.0000
2:210015972:GACAT:Gacceptor_gain1.0000
2:210016109:GAAG:Gdonor_gain1.0000
2:210016110:AAGG:Adonor_loss1.0000
2:210016111:AGG:Adonor_loss1.0000
2:210016113:G:Cdonor_loss1.0000
2:210016114:T:Adonor_loss1.0000
2:210002779:G:GTdonor_gain0.9900
2:210016113:G:GGdonor_gain0.9900
2:210016500:GTTAC:Gacceptor_loss0.9900
2:210016501:TTACA:Tacceptor_loss0.9900
2:210016502:TACAG:Tacceptor_loss0.9900
2:210016503:ACAG:Aacceptor_loss0.9900
2:210016504:CAGG:Cacceptor_loss0.9900
2:210016505:A:ACacceptor_loss0.9900
2:210016506:G:GAacceptor_loss0.9900
2:210016648:G:GTdonor_gain0.9900
2:210009656:GGC:Gacceptor_gain0.9800
2:210016538:T:Gdonor_gain0.9800
2:210016637:CAAAG:Cdonor_loss0.9800
2:210016639:AAGGT:Adonor_loss0.9800
2:210016640:AG:Adonor_loss0.9800

AlphaMissense

1521 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:210002764:C:GH35D1.000
2:210002771:A:TD37V1.000
2:210002772:C:AD37E1.000
2:210002772:C:GD37E1.000
2:210002779:G:CD40H1.000
2:210016050:C:GH94D1.000
2:210016586:T:CM141T1.000
2:210016587:G:AM141I1.000
2:210016587:G:CM141I1.000
2:210016587:G:TM141I1.000
2:210016601:G:AG146E1.000
2:210017518:G:CD175H1.000
2:210017519:A:TD175V1.000
2:210017520:T:AD175E1.000
2:210017520:T:GD175E1.000
2:210017521:G:CG176R1.000
2:210017522:G:AG176D1.000
2:210017522:G:TG176V1.000
2:210002684:G:AG8D0.999
2:210002690:C:TS10F0.999
2:210002696:T:AL12H0.999
2:210002696:T:CL12P0.999
2:210002764:C:AH35N0.999
2:210002768:T:CL36P0.999
2:210002770:G:AD37N0.999
2:210002770:G:CD37H0.999
2:210002770:G:TD37Y0.999
2:210002771:A:CD37A0.999
2:210002771:A:GD37G0.999
2:210002780:A:TD40V0.999

dbSNP variants (sampled 300 via entrez): RS1000273422 (2:210017617 C>A,G,T), RS1000278047 (2:210018577 A>G), RS1000318665 (2:210005324 C>T), RS1000452015 (2:210001169 A>C), RS1000501509 (2:210016472 G>A,C), RS1000565894 (2:210017924 T>C), RS1000727111 (2:210013995 T>C), RS1000763373 (2:210013675 C>G,T), RS1000768950 (2:210010292 T>C), RS1000873459 (2:210021443 A>T), RS1000967335 (2:210022686 A>C,G), RS1001607964 (2:210011776 A>G,T), RS1001754714 (2:210005694 C>T), RS1002086917 (2:210004348 TG>T), RS1002290536 (2:210016994 C>T)

Disease associations

OMIM: gene MIM:180480 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006249_98Serum metabolite levels2.000000e-24
GCST006249_99Serum metabolite levels3.000000e-33

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7570090RPE0.000

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, decreases expression2
bisphenol Sincreases expression, increases methylation2
Hydrogen Peroxideaffects expression, increases expression2
Tretinoindecreases expression, increases expression2
aristolochic acid Idecreases expression, increases expression1
bisphenol Fincreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
sodium arsenatedecreases expression1
cobaltous chloridedecreases expression1
manganese chlorideincreases abundance, increases expression1
methacrylaldehydeincreases expression, affects cotreatment1
beta-methylcholineaffects expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases expression1
Air Pollutants, Occupationaldecreases expression1
Arsenicincreases abundance, increases expression1
Doxorubicindecreases expression1
Ivermectindecreases expression1
Manganeseincreases abundance, increases expression1
Nickeldecreases expression1
Ozoneaffects cotreatment, increases expression1
Plant Extractsaffects cotreatment, increases expression1
Quercetindecreases expression1
Valproic Acidincreases expression1
Cadmium Chlorideincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B3G6Abcam HEK293T RPE KOTransformed 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.