RPEL1

Summary

RPEL1 (ribulose-5-phosphate-3-epimerase like 1, HGNC:45241) is a protein-coding gene on chromosome 10q24.33, encoding Ribulose-phosphate 3-epimerase-like protein 1 (Q2QD12). Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.

Predicted to enable D-ribulose-phosphate 3-epimerase activity and metal ion binding activity. Predicted to be involved in carbohydrate metabolic process and pentose-phosphate shunt, non-oxidative branch. Predicted to be active in cytosol.

Source: NCBI Gene 729020 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 41 total
• MANE Select transcript: NM_001143909

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:45241
Approved symbol	RPEL1
Name	ribulose-5-phosphate-3-epimerase like 1
Location	10q24.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000235376
Ensembl biotype	protein_coding
Entrez	729020

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000441178

RefSeq mRNA: 1 — MANE Select: NM_001143909 NM_001143909

CCDS: CCDS65929

Canonical transcript exons

ENST00000441178 — 1 exons

Exon	Start	End
ENSE00002292755	103245887	103248016

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 76.85.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.85	gold quality
superior frontal gyrus	UBERON:0002661	47.32	silver quality
primary visual cortex	UBERON:0002436	47.11	silver quality
stromal cell of endometrium	CL:0002255	39.28	gold quality
vermiform appendix	UBERON:0001154	38.87	silver quality
cerebellum	UBERON:0002037	37.91	gold quality
cerebellar cortex	UBERON:0002129	37.72	gold quality
cerebellar hemisphere	UBERON:0002245	37.27	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
skeletal muscle tissue	UBERON:0001134	36.37	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right hemisphere of cerebellum	UBERON:0014890	35.03	gold quality
mucosa of transverse colon	UBERON:0004991	34.64	gold quality
placenta	UBERON:0001987	34.46	gold quality
muscle tissue	UBERON:0002385	34.39	gold quality
bone marrow	UBERON:0002371	32.88	gold quality
duodenum	UBERON:0002114	32.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
endometrium	UBERON:0001295	31.59	gold quality
lymph node	UBERON:0000029	31.56	gold quality
leukocyte	CL:0000738	31.15	gold quality
monocyte	CL:0000576	30.96	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
adrenal tissue	UBERON:0018303	30.89	gold quality
corpus callosum	UBERON:0002336	30.80	gold quality
cortex of kidney	UBERON:0001225	30.79	gold quality
Brodmann (1909) area 9	UBERON:0013540	30.58	gold quality
liver	UBERON:0002107	30.52	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.35
E-ENAD-17	no	56.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting RPEL1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-142-3P	99.62	71.30	974
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-4742-5P	98.89	68.41	1542

Literature-anchored findings (GeneRIF, showing 1)

• Associations of RPEL1 and miR-1307 gene polymorphisms with disease susceptibility, glucocorticoid efficacy, anxiety, depression, and health-related quality of life in Chinese systemic lupus erythematosus patients. (PMID:36194484)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rpe	ENSDARG00000005251
mus_musculus	Rpe	ENSMUSG00000026005
rattus_norvegicus	Rpe	ENSRNOG00000038085
drosophila_melanogaster	Rpe	FBGN0050499
caenorhabditis_elegans		WBGENE00017272

Paralogs (1): RPE (ENSG00000197713)

Protein

Protein identifiers

Ribulose-phosphate 3-epimerase-like protein 1 — Q2QD12 (reviewed: Q2QD12)

Alternative names: Ribulose-5-phosphate-3-epimerase-like protein 1

All UniProt accessions (1): Q2QD12

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.

Miscellaneous. According to some authors, RPEL1 is a RPE retrogene on chromosome 2 which is likely to be functional.

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

RefSeq proteins (1): NP_001137381* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000056	Ribul_P_3_epim-like	Family
IPR011060	RibuloseP-bd_barrel	Homologous_superfamily
IPR013785	Aldolase_TIM	Homologous_superfamily
IPR026019	Ribul_P_3_epim	Family

Pfam: PF00834

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (12 total): binding site 9, active site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2QD12-F1	96.53	0.93

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; 197–198; 10; 35; 37; 70; 70; 146–149; 175–177

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

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

MSigDB gene sets: 36 (showing top): GOBP_NADPPLUS_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, 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, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, KEGG_PENTOSE_PHOSPHATE_PATHWAY, GOBP_ALDEHYDE_METABOLIC_PROCESS, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, GOMF_RACEMASE_AND_EPIMERASE_ACTIVITY, GOMF_ISOMERASE_ACTIVITY, KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS, GOBP_PENTOSE_PHOSPHATE_SHUNT_NON_OXIDATIVE_BRANCH

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

GO Molecular Function (4): D-ribulose-phosphate 3-epimerase activity (GO:0004750), metal ion binding (GO:0046872), isomerase activity (GO:0016853), racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)

GO Cellular Component (1): cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Metabolism of carbohydrates and carbohydrate derivatives	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
D-ribulose-phosphate 3-epimerase activity	1
ribose-5-phosphate isomerase activity	1
transaldolase activity	1
transketolase activity	1
generation of precursor metabolites and energy	1
pentose-phosphate shunt	1
glyceraldehyde-3-phosphate metabolic process	1
NADPH regeneration	1
pentose-phosphate shunt, oxidative branch	1
pentose-phosphate shunt, non-oxidative branch	1
glucose 6-phosphate metabolic process	1
racemase and epimerase activity, acting on carbohydrates and derivatives	1
cation binding	1
catalytic activity	1
racemase and epimerase activity	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1458 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPEL1	RPIA	P49247	810
RPEL1	TKT	P29401	783
RPEL1	TKTL1	P51854	764
RPEL1	TKTL2	Q9H0I9	761
RPEL1	TALDO1	P37837	745
RPEL1	TPI1	P00938	677
RPEL1	PGD	P52209	671
RPEL1	PGLS	O95336	667
RPEL1	GPI	P06744	666
RPEL1	PGK2	P07205	623
RPEL1	H6PD	O95479	607
RPEL1	FBP1	P09467	592
RPEL1	FBP2	O00757	591
RPEL1	G6PD	P11413	571
RPEL1	PRPS2	P11908	563

IntAct

5 interactions, top by confidence:

A	B	Type	Score
M		psi-mi:“MI:0914”(association)	0.350
RPEL1	APAF1	psi-mi:“MI:0914”(association)	0.350
DDX28	UBA6	psi-mi:“MI:0914”(association)	0.350
GAB2	UBA6	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): DUPD1 (Affinity Capture-MS), APAF1 (Affinity Capture-MS), BANP (Affinity Capture-MS), RPEL1 (Negative Genetic), RPEL1 (Negative Genetic)

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.

A	Effect	B	Mechanism
RPEL1	“down-regulates quantity”	“D-ribulose 5-phosphate”	“chemical modification”
RPEL1	“up-regulates quantity”	“D-xylulose 5-phosphate(2-)”	“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1525 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:103246273:T:C	F93L	0.949
10:103246275:T:A	F93L	0.949
10:103246275:T:G	F93L	0.949
10:103246123:T:C	F43L	0.928
10:103246125:T:A	F43L	0.928
10:103246125:T:G	F43L	0.928
10:103246435:T:C	F147L	0.915
10:103246437:T:A	F147L	0.915
10:103246437:T:G	F147L	0.915
10:103246450:T:C	F152L	0.891
10:103246452:C:A	F152L	0.891
10:103246452:C:G	F152L	0.891
10:103246495:T:C	F167L	0.886
10:103246497:C:A	F167L	0.886
10:103246497:C:G	F167L	0.886
10:103246141:T:C	F49L	0.881
10:103246143:T:A	F49L	0.881
10:103246143:T:G	F49L	0.881
10:103246192:T:C	F66L	0.873
10:103246194:C:A	F66L	0.873
10:103246194:C:G	F66L	0.873
10:103246116:T:A	D40E	0.854
10:103246116:T:G	D40E	0.854
10:103246114:G:C	D40H	0.853
10:103246107:T:A	D37E	0.851
10:103246107:T:G	D37E	0.851
10:103246334:T:C	M113T	0.847
10:103246419:G:A	M141I	0.847
10:103246419:G:C	M141I	0.847
10:103246419:G:T	M141I	0.847

dbSNP variants (sampled 300 via entrez): RS1002713277 (10:103244671 T>C), RS1003293098 (10:103246454 T>C), RS1003710516 (10:103248273 C>A), RS1003720294 (10:103247964 T>C), RS1004715452 (10:103244298 G>C), RS1004799013 (10:103246818 T>C,G), RS1005830445 (10:103247832 A>G), RS1006133544 (10:103245787 C>G), RS1006760249 (10:103243957 C>T), RS1006792763 (10:103244380 G>T), RS1008405672 (10:103245145 C>G), RS1008510739 (10:103244043 C>A,T), RS1010317135 (10:103244512 T>A,G), RS1010764451 (10:103244717 G>A,T), RS1010982442 (10:103247314 T>A)

Disease associations

OMIM: gene `` | 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):

Study	Trait	p-value
GCST004521_172	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST005979_16	Systolic blood pressure	3.000000e-16
GCST006009_7	Pulse pressure	5.000000e-17
GCST006010_26	Mean arterial pressure	6.000000e-10
GCST006803_4	Schizophrenia	7.000000e-18
GCST007327_199	Smoking status (ever vs never smokers)	5.000000e-08
GCST007327_98	Smoking status (ever vs never smokers)	1.000000e-09
GCST008361_2	Response to cognitive-behavioural therapy in major depressive disorder	2.000000e-06
GCST010226_5	Cortical surface area (global PC1)	2.000000e-09
GCST012009_5	Thalamus volume	1.000000e-09

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0006340	mean arterial pressure
EFO:0004318	smoking behavior
EFO:0007820	cognitive behavioural therapy
EFO:0008381	total cortical area measurement
EFO:0006935	thalamus volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.