RPE

ribulose-5-phosphate-3-epimerase

Basic information

Region (hg38): 2:210002564-210022260

Links

ENSG00000197713 ∙ NCBI:6120 ∙ OMIM:180480 ∙ HGNC:10293 ∙ Uniprot:Q96AT9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	3	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
2-210009659-A-G		not specified	Uncertain significance (Mar 08, 2024)
2-210016078-C-G		not specified	Uncertain significance (Jan 11, 2023)
2-210017837-C-T			Likely benign (Oct 01, 2023)
2-210019736-A-G		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPE	protein_coding	protein_coding	ENST00000359429	6	19012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000252	0.784	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	117	134	0.873	0.00000651	1518
Missense in Polyphen		37	47.562	0.77792		557
Synonymous	0.765	39	45.6	0.856	0.00000222	431
Loss of Function	1.10	7	10.9	0.642	5.27e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rpe

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