title: Updated genetic testing of Italian patients referred with a clinical diagnosis of primary hyperoxaluria.
abstract: BACKGROUND
  Primary hyperoxaluria (PH) is a rare autosomal recessive disease commonly arising in childhood and presenting with nephrolithiasis, nephrocalcinosis and/or chronic renal failure. Three genes are currently known as responsible: alanine-glyoxylate aminotransferase (AGXT, PH type 1), glyoxylate reductase/hydroxypyruvate reductase (GRHPR, PH type 2), and 4-hydroxy-2-oxoglutarate aldolase (HOGA1, PH type 3). In our Centre, at the end of 2014 molecular diagnosis of PH1 had been performed in 80 patients, while one patient received a PH2 diagnosis.
  
  
  METHODS
  Fifteen patients referred to our Centre and suspected to have PH on clinical grounds were negative for pathogenic variants in the entire coding sequence and exon-intron boundaries of the AGXT gene. Therefore, we extended the analysis to the AGXT promoter region and the GRHPR and HOGA1 genes.
  
  
  RESULTS
  Two patients were heterozygous for two novel AGXT-promoter variants (c.-647C > T, c.-424C > T) that were probably non pathogenic. One patient was homozygous for a novel HOGA1 variant of intron 2 (c.341-81delT), whose pathogenicity predicted by in silico splicing tools was not confirmed by a minigene splicing assay in COS-7 and HEK293T cells.
  
  
  CONCLUSIONS
  New genetic subtypes of PH can be hypothesized in our patients, that may be caused by mutations in other gene encoding proteins of glyoxylate metabolism. Alternatively, some kind of mutations (e.g., deletions/duplications, deep intronic splicing regulatory variants) could be missed in a few cases, similarly to other genetic diseases.
authors.affiliation: Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Regione Gonzole 10, 10040, Orbassano, TO, Italy. alessandraelisapelle@gmail.com.|Medical Genetics Unit, San Luigi University Hospital, Orbassano, Italy. alessandraelisapelle@gmail.com.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Pelle
authors.affiliation: Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Regione Gonzole 10, 10040, Orbassano, TO, Italy.|Medical Genetics Unit, San Luigi University Hospital, Orbassano, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Cuccurullo
authors.affiliation: Department of Medical Sciences, Città della Salute e della Scienza, University of Torino, Turin, Italy.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Mancini
authors.affiliation: Medical Genetics Unit, San Luigi University Hospital, Orbassano, Italy.
authors.forename: Regina
authors.initials: R
authors.lastname: Sebastiano
authors.affiliation: Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Stallone
authors.affiliation: Pediatric Nephrology, Dialysis and Transplant Unit, Department of Pediatrics, University of Padova, Padua, Italy.
authors.forename: Susanna
authors.initials: S
authors.lastname: Negrisolo
authors.affiliation: Pediatric Nephrology, Dialysis and Transplant Unit, Department of Pediatrics, University of Padova, Padua, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Benetti
authors.affiliation: Nephrology Dialysis Transplantation Unit, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy.
authors.forename: Licia
authors.initials: L
authors.lastname: Peruzzi
authors.affiliation: S.C. Laboratorio Centrale, A. O. Ordine Mauriziano, Turin, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Petrarulo
authors.affiliation: Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Regione Gonzole 10, 10040, Orbassano, TO, Italy.|Medical Genetics Unit, San Luigi University Hospital, Orbassano, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: De Marchi
authors.affiliation: Fondazione Scientifica, A. O. Ordine Mauriziano, Turin, Italy.
authors.forename: Martino
authors.initials: M
authors.lastname: Marangella
authors.affiliation: Department of Medical Sciences, Città della Salute e della Scienza, University of Torino, Turin, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Amoroso
authors.affiliation: Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Regione Gonzole 10, 10040, Orbassano, TO, Italy.|Medical Genetics Unit, San Luigi University Hospital, Orbassano, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Giachino
authors.affiliation: Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Regione Gonzole 10, 10040, Orbassano, TO, Italy.
authors.forename: Giorgia
authors.initials: G
authors.lastname: Mandrile
mesh_terms: D000293:Adolescent; D000328:Adult; D000429:Alcohol Oxidoreductases / Q000235:genetics*; D000818:Animals; D019556:COS Cells; D002648:Child; D002675:Child, Preschool; D002522:Chlorocebus aethiops; D004252:DNA Mutational Analysis; D005091:Exons; D005260:Female; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods*; D057809:HEK293 Cells; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D006960:Hyperoxaluria, Primary / Q000175:diagnosis* / Q000201:enzymology / Q000235:genetics* / Q000628:therapy; D007438:Introns; D007558:Italy; D007668:Kidney / Q000503:physiopathology; D008297:Male; D009154:Mutation; D007652:Oxo-Acid-Lyases / Q000235:genetics*; D010641:Phenotype; D011237:Predictive Value of Tests; D011401:Promoter Regions, Genetic; D000637:Transaminases / Q000235:genetics*; D014162:Transfection; D055815:Young Adult
chemical_list: D000429:Alcohol Oxidoreductases; C020830:glyoxylate reductase; D000637:Transaminases; C019635:Alanine-glyoxylate transaminase; D007652:Oxo-Acid-Lyases; C021415:4-hydroxy-2-oxoglutarate aldolase
keywords: AGXT; GRHPR; Glyoxylate metabolism; HOGA1; Primary hyperoxaluria