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GeneBe

RPE

ribulose-5-phosphate-3-epimerase

Basic information

Region (hg38): 2:210002564-210022260

Links

ENSG00000197713NCBI:6120OMIM:180480HGNC:10293Uniprot:Q96AT9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPE gene.

  • not provided (1 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPE gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 1 1 0

Variants in RPE

This is a list of pathogenic ClinVar variants found in the RPE region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-210016078-C-G Inborn genetic diseases Uncertain significance (Jan 11, 2023)2475535
2-210017837-C-T Likely benign (Oct 01, 2023)2651858

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPEprotein_codingprotein_codingENST00000359429 619012
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0002520.7841257270201257470.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5211171340.8730.000006511518
Missense in Polyphen3747.5620.77792557
Synonymous0.7653945.60.8560.00000222431
Loss of Function1.10710.90.6425.27e-7124

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.0001500.000141
Middle Eastern0.000.00
South Asian0.00003310.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate. {ECO:0000269|PubMed:20923965}.;
Pathway
Pentose phosphate pathway - Homo sapiens (human);Pentose and glucuronate interconversions - Homo sapiens (human);Pentose Phosphate Pathway;Glucose-6-phosphate dehydrogenase deficiency;Ribose-5-phosphate isomerase deficiency;Transaldolase deficiency;Pentose Phosphate Pathway;Pentose phosphate pathway (hexose monophosphate shunt);Metabolism of carbohydrates;Metabolism;pentose phosphate pathway (non-oxidative branch);pentose phosphate pathway (Consensus)

Recessive Scores

pRec
0.326

Intolerance Scores

loftool
0.359
rvis_EVS
-0.05
rvis_percentile_EVS
49.76

Haploinsufficiency Scores

pHI
0.718
hipred
N
hipred_score
0.273
ghis
0.650

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.958

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpe
Phenotype

Zebrafish Information Network

Gene name
rpe
Affected structure
otolith
Phenotype tag
abnormal
Phenotype quality
malformed

Gene ontology

Biological process
carbohydrate metabolic process;pentose-phosphate shunt;pentose-phosphate shunt, non-oxidative branch;pentose catabolic process;cellular carbohydrate metabolic process
Cellular component
cytosol;extracellular exosome
Molecular function
ribulose-phosphate 3-epimerase activity;identical protein binding;protein homodimerization activity;metal ion binding