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Undiagnosed metabolic disorders

Gene: RPIA

Green List (high evidence)

RPIA (ribose 5-phosphate isomerase A)
EnsemblGeneIds (GRCh38): ENSG00000153574
EnsemblGeneIds (GRCh37): ENSG00000153574
OMIM: 180430, Gene2Phenotype
RPIA is in 5 panels

2 reviews

Sarah Leigh (Genomics England Curator)

Review by Konstantinos Varvagiannis for the Genetic Epilepsy syndromes panel. 9 Dec 2018, 1:44 a.m.
Panel version: 0.1488
Biallelic pathogenic variants in RPIA cause Ribose 5-phosphate isomerase deficiency, MIM 608611. PMID: 14988808 is the first report on the disorder with molecular (incl. genetic) confirmation of the diagnosis. A patient initially investigated for early developmental delay, leukoencephalopathy, seizures with onset at 4 years, with subsequent neurologic regression and peripheral neuropathy at the age of 7, was suspected to have a disorder of the pentose phosphate pathway on the basis of highly elevated polyols on brain MRS and body fluid analysis. Reduced ribose 5-phosphate isomerase activity was shown in fibroblasts. Genetic testing demonstrated the presence of a missense (NM_144563.2:c.404C>T or p.Ala135Val - previously referred to as A61V) as well as a frameshift variant (NM_144563.2:c.762delG or p.Asn255Ilefs). Additional extensive supportive functional studies were published a few years later (PMID: 20499043). [This patient was initially described in PMID: 10589548]. PMID: 28801340 is a report on a second patient. This individual presented with delayed early development (independent walking and speech achieved at 2 and 5 years respectively), seizures and regression at the age of 7 with MRI white matter abnormalities. Review of magnetic resonance spectroscopy (MRS) was suggestive of elevated polyols (arabitol and ribitol). In line with this, genetic testing revealed a homozygous missense variant in RPIA (NM_144563.2:c.592T>C or p.Phe198Leu). Urine analysis confirmed elevated excretion of polyols, thus confirming the diagnosis. PMID: 30088433 reports on a boy with neonatal onset leukoencephalopathy and developmental delay having undergone early metabolic testing and aCGH (the latter at the age of 16 months). Persistance of his delay motivated exome sequencing at the age of approx. 4.5 years which demonstrated 2 RPIA variants (NM_144563.2:c.253G>A or p.Ala85Thr and NM_144563.2:c.347-1G>A). Measurement of ribitol and arabitol in urine demonstrated significant elevations (>20x) consistent with this diagnosis. 2 of the 3 patients described in the literature presented seizures. As a result this gene can be considered for inclusion in this panel as amber. [This gene is also present in the Undiagnosed metabolic disorders gene panel as red. Please consider upgrade based on these further publications.]. Sources: Literature
Created: 11 Dec 2018, 11:31 a.m.
Comment on list classification: Based on additional variants reported in PMIDs 28801340; 30088433.
Created: 11 Dec 2018, 11:21 a.m.

Olivia Niblock (Genomics England Curator)

Red List (low evidence)

Associated with phenotype in OMIM, not in G2P. At least 2 variants reported in one case, supporting in vitro data in yeast model presented in PMID 20499043. Over expression of RPIA can induce oncogenes in human hepatocellular carcinoma (PMID 25429733)
Created: 23 Feb 2017, 5:15 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
?Ribose 5-phosphate isomerase deficiency 608611

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Ribose-5-phosphate isomerase deficiency (Disorders of pentose metabolism)
  • ?Ribose 5-phosphate isomerase deficiency 608611
OMIM
180430
Clinvar variants
Variants in RPIA
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

11 Dec 2018, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: RPIA were set to 27604308

11 Dec 2018, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: rpia has been classified as Green List (High Evidence).

11 Dec 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: rpia has been classified as Amber List (Moderate Evidence).

27 Feb 2017, Gel status: 1

panel promoted to version 1

Sarah Leigh (Genomics England Curator)

Construction of “Undiagnosed Metabolic Disorders” (UDM) panel • The 614 genes from the neurometabolic gene panel (PMID: 27604308) added • Green genes downloaded from V1 metabolic panels (Cerebral folate deficiency, Congenital disorders of glycosylation, Hyperammonaemia, Ketotic hypoglycaemia, Mitochondrial disorders, Mucopolysaccharideosis, Gaucher, Fabry, Peroxisomal disorders), sources replaced with "Expert review green", then loaded as a review onto UDM panel, resulting in 367 green genes and 333 red (therefore 86 new green genes included from the additional metabolic panels that weren't previously on the UDM panel) • Downloaded green genes from all panels. Removed genes from none V1 panels. Removed genes from the metabolic panels mentioned above. Compared the remaining genes with the red genes from UDM panel. Loaded as an "Expert review Amber" review to the overlapping genes, (the panel name where the genes came from was used as the phenotype) • Used variant information from PMID 27604308 to review the genes on this panel • Reviewed genes on UDM panel with genes from Emory "Inherited Metabolic Disorders: Sequencing Panel" and UKGTN “Inborn Errors of Metabolism 226 panel”, changing status where appropriate, added 14 UKGTN genes that had not be listed before • Review 10 red genes that had not previously been reviewed, 4/10 were reclassified as green • Review the remaining 145 red genes that had not previously been reviewed (shared between reviewers EM, RF, LD, AT, HB, ON & SL), resulting in 60 green, 11 amber, 70 red, 4 I don’t know reviews) • Reviewed genes from PMID: 24816252 as a publication to genes found in the Inborn error or metabolism Genes metabolomics GWAS paper (figure 5). 2 new genes added

24 Feb 2017, Gel status: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

RPIA was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Red Model of inheritance for gene RPIA was set to BIALLELIC, autosomal or pseudoautosomal

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

RPIA was added to Undiagnosed metabolic disorderspanel. Sources: Literature

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

RPIA was created by sleigh