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GeneBe

RPIA

ribose 5-phosphate isomerase A

Basic information

Region (hg38): 2:88691672-88750929

Links

ENSG00000153574NCBI:22934OMIM:180430HGNC:10297Uniprot:P49247AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ribose-5-P isomerase deficiency (Moderate), mode of inheritance: AR
  • ribose-5-P isomerase deficiency (Supportive), mode of inheritance: AR
  • ribose-5-P isomerase deficiency (Strong), mode of inheritance: AR
  • ribose-5-P isomerase deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ribose 5-phosphate isomerase deficiencyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Neurologic14988808

ClinVar

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

  • not provided (50 variants)
  • Deficiency of ribose-5-phosphate isomerase (38 variants)
  • Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPIA 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
1
clinvar
13
clinvar
4
clinvar
18
missense
2
clinvar
28
clinvar
1
clinvar
1
clinvar
32
nonsense
1
clinvar
2
clinvar
3
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
?
0
non coding
?
16
clinvar
8
clinvar
3
clinvar
27
Total 2 4 46 22 8

Highest pathogenic variant AF is 0.0000197

Variants in RPIA

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

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

Position Type Phenotype Significance ClinVar
2-88691682-C-A Deficiency of ribose-5-phosphate isomerase Uncertain significance (Jan 12, 2018)897553
2-88691702-C-T Likely pathogenic (Apr 18, 2023)2662889
2-88691703-A-G Deficiency of ribose-5-phosphate isomerase Conflicting classifications of pathogenicity (May 21, 2021)897554
2-88691708-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2021)2254461
2-88691709-C-T Uncertain significance (Jan 03, 2022)1408917
2-88691710-C-A Likely benign (Jul 19, 2022)1925409
2-88691710-C-G Likely benign (Jul 17, 2022)2055832
2-88691710-C-T Likely benign (Nov 08, 2022)748412
2-88691714-C-T Inborn genetic diseases Uncertain significance (Mar 06, 2023)2458836
2-88691725-C-T Likely benign (Aug 13, 2022)1900381
2-88691753-C-A Deficiency of ribose-5-phosphate isomerase Uncertain significance (Jan 12, 2018)337428
2-88691755-C-T Deficiency of ribose-5-phosphate isomerase Conflicting classifications of pathogenicity (Aug 09, 2022)897555
2-88691772-C-G Uncertain significance (Nov 28, 2021)1978867
2-88691782-C-T Benign (Nov 01, 2023)742902
2-88691791-G-A Likely benign (Jul 15, 2022)2064631
2-88691804-C-A Benign (Aug 26, 2022)786863
2-88691819-G-T Uncertain significance (Mar 22, 2022)1911125
2-88691841-A-G Inborn genetic diseases Uncertain significance (Jul 25, 2023)2613644
2-88691844-C-T Inborn genetic diseases Uncertain significance (Dec 19, 2022)2207838
2-88691852-C-T Uncertain significance (Jun 13, 2022)1980521
2-88691875-C-T Deficiency of ribose-5-phosphate isomerase Uncertain significance (Jan 13, 2018)897556
2-88691891-T-TC Uncertain significance (Aug 20, 2022)2021430
2-88691895-A-G Uncertain significance (May 23, 2023)1303034
2-88691897-A-G Inborn genetic diseases Uncertain significance (Jul 16, 2021)2238161
2-88691910-C-A Uncertain significance (Nov 08, 2022)2057992

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPIAprotein_codingprotein_codingENST00000283646 959291
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001430.9671247800171247970.0000681
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9591471840.8010.000009672017
Missense in Polyphen3662.2490.57832708
Synonymous-0.5607771.01.080.00000379618
Loss of Function1.91917.70.5100.00000107168

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001840.000184
Ashkenazi Jewish0.000.00
East Asian0.0001190.000111
Finnish0.00004640.0000464
European (Non-Finnish)0.00004680.0000441
Middle Eastern0.0001190.000111
South Asian0.0001340.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Disease
DISEASE: Ribose 5-phosphate isomerase deficiency (RPID) [MIM:608611]: A patient has been described with a deficiency of ribose 5-phosphate isomerase who presented with leukoencephalopathy and peripheral neuropathy. Proton magnetic resonance spectroscopy of the brain revealed a highly elevated level of the polyols ribitol and D-arabitol, which were subsequently also found in high concentrations in body fluids. Deficient activity of RPIA, one of the pentose phosphate pathway enzymes, has been demonstrated in fibroblasts. {ECO:0000269|PubMed:14988808}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Pentose phosphate pathway - Homo sapiens (human);Warburg Effect;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 cycle;pentose phosphate pathway (non-oxidative branch);pentose phosphate pathway (Consensus)

Recessive Scores

pRec
0.461

Intolerance Scores

loftool
0.485
rvis_EVS
-0.16
rvis_percentile_EVS
41.25

Haploinsufficiency Scores

pHI
0.586
hipred
N
hipred_score
0.455
ghis
0.584

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.994

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpia
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;

Gene ontology

Biological process
D-ribose metabolic process;pentose-phosphate shunt;pentose-phosphate shunt, non-oxidative branch
Cellular component
cytosol;intracellular membrane-bounded organelle
Molecular function
ribose-5-phosphate isomerase activity;protein binding;identical protein binding;monosaccharide binding