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Blueprint Genetics Nephrolithiasis Panel

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Blueprint Genetics Nephrolithiasis Panel Nephrolithiasis Panel Test code: KI2201 Is a 35 gene panel that includes assessment of non-coding variants. Is ideal for patients with nephrolithiasis / hypercalciuria. About Nephrolithiasis Nephrolithiasis (kidney stone disease), is a frequent disorder with a prevalence between 5 and 10% in the general population. It is usually associated with a metabolic abnormality that may include hypercalciuria, hyperphosphaturia, hyperoxaluria, hypocitraturia, hyperuricosuria, cystinuria, a low urinary volume and a defect in urinary acidification. Genetic as well as environmental factors are thought to contribute to its pathogenesis. Hypercalciuric nephrolithiasis is a familial disorder in over 35% of patients. Monogenic forms of hypercalciuric nephrolithiasis include Bartter syndrome, Dent’s disease, autosomal dominant hypocalcemic hypercalciuria (ADHH), hypercalciuric nephrolithiasis with hypophosphatemia, and familial hypomagnesemia with hypercalciuria. Genes associated with nephrolithiasis encode for proteins including a number of transporters, channels and receptors that are involved in regulating the renal tubular reabsorption of calcium, phosphate and the activity of precipitation inhibitors. The majority (65% to 75%) of stones are composed of either pure or mostly of calcium salts, including those of calcium oxalate, mixed calcium oxalate with uric acid, and calcium phosphate (brushite). Uric acid, cystine, and magnesium ammonium phosphate (struvite) compose the remainder of the stones. Composition of the stone reflects metabolic abnormalities in the urine. The treatment is based on diagnosis, and genetic testing may help as biochemical testing does not usually lead to an accurate molecular diagnosis. Environmental and especially dietary factors are important in primary as well as in secondary prevention. Availability 4 weeks Gene Set Description Genes in the Nephrolithiasis Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ADCY10 Absorptive hypercalciuria AD 6 AGXT Hyperoxaluria AR 190 205 ALPL Odontohypophosphatasia, Hypophosphatasia perinatal lethal, infantile, AD/AR 78 291 juvenile and adult forms APRT Adenine phosphoribosyltransferase deficiency AR 11 47 ATP6V0A4 Renal tubular acidosis, distal AR 16 84 ATP6V1B1 Renal tubular acidosis with deafness AR 15 56 CA2 Osteopetrosis, with renal tubular acidosis AR 9 31 CASR Hypocalcemia, Neonatal hyperparathyroidism, Familial Hypocalciuric AD/AR 104 396 hypercalcemia with transient Neonatal hyperparathyroidism CLCN5 Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis, XL 48 272 Hypophosphatemic rickets,, Nephrolithiasis, I, Dent disease https://blueprintgenetics.com/ CLDN16 Hypomagnesemia, renal AR 21 62 CLDN19 Hypomagnesemia, renal AR 7 20 CYP24A1 Hypercalcemia, infantile 1 AR 8 40 FAM20A Amelogenesis imperfecta (Enamel-renal syndrome) AR 19 41 GNA11 Hypocalcemia, Hypocalciuric hypercalcemia AD 11 11 GPHN Hyperekplexia, Molybdenum cofactor deficiency AD/AR 35 20 GRHPR Hyperoxaluria AR 60 40 HNF4A Congenital hyperinsulinism, diazoxide-responsive, Maturity onset diabetes AD 32 147 of the young, Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young HOGA1 Hyperoxaluria AD/AR 37 33 HPRT1 Lesch-Nyhan syndrome, Kelley-Seegmiller syndrome XL 72 427 KCNJ1 Bartter syndrome, antenatal AR 11 66 MOCOS Xanthinuria, type II AR 3 5 MOCS1* Molybdenum cofactor deficiency AR 7 35 OCRL Lowe syndrome, Dent disease XL 47 264 SLC12A1 Bartter syndrome, antenatal AR 18 81 SLC22A12 Hypouricemia, renal 1 AR 8 40 SLC26A1 Nephrolithiasis, calcium oxalate AR 18 5 SLC2A9 Hypouricemia, renal, 2 AD/AR 9 20 SLC34A1 Nephrolithiasis/osteoporosis, hypophosphatemic, Fanconi renotubular AD/AR 22 29 syndrome, Hypercalcemia, infantile 2 SLC34A3 Hypophosphatemic rickets with hypercalciuria AR 22 38 SLC3A1 Cystinuria AR 26 241 SLC4A1 Spherocytosis, Ovalcytosis, Renal tubular acidosis, distal, with hemolytic AD/AR/BG 38 122 anemia, Cryohydrocytosis, Acanthocytosis, Band 3 Memphis SLC7A9 Cystinuria AD/AR 24 159 SLC9A3R1 Nephrolithiasis/osteoporosis, hypophosphatemic, 2 AD 7 VDR Vitamin D-dependent rickets AD/AR 17 66 XDH Xanthinuria, type I AR 10 21 *Some regions of the gene are duplicated in the genome. Read more. # The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads. https://blueprintgenetics.com/ The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#). Due to possible limitations these genes may not be available as single gene tests. Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Mitomap databases. Non-coding disease causing variants covered by the panel Gene Genomic location HGVS RefSeq RS-number HG19 ALPL Chr1:21835920 c.-195C>T NM_000478.4 ALPL Chr1:21896764 c.793-30_793-11delGGCATGTGCTGACACAGCCC NM_000478.4 CASR Chr3:121994640 c.1378-19A>C NM_001178065.1 CLDN16 Chr3:190127678 c.785-14T>G NM_006580.3 HNF4A Chr20:42984253 c.-192C>G NM_175914.4 HNF4A Chr20:42984264 c.-181G>A NM_175914.4 HNF4A Chr20:42984271 c.-174T>C NM_175914.4 HNF4A Chr20:42984276 c.-169C>T NM_175914.4 HNF4A Chr20:42984299 c.-146T>C NM_175914.4 HNF4A Chr20:42984309 c.-136A>G NM_175914.4 HNF4A Chr20:43036000 c.291-21A>G NM_000457.4 HPRT1 ChrX:133594415 c.27+47C>T NM_000194.2 HPRT1 ChrX:133625464 c.402+1229A>G NM_000194.2 HPRT1 ChrX:133628822 c.485+1202T>A NM_000194.2 HPRT1 ChrX:133632625 c.533-13T>G NM_000194.2 MOCS1 Chr6:39874534 c.*365_*366delAG NM_005943.5 rs397518419 MOCS1 Chr6:39876810 c.*7+6T>C NM_005943.5 MOCS1 Chr6:39894006 c.251-418delT NM_005943.5 OCRL ChrX:128674707 c.40-14A>G NM_000276.3 OCRL ChrX:128687279 c.239-4023A>G NM_000276.3 OCRL ChrX:128696350 c.940-11G>A NM_000276.3 SLC12A1 Chr15:48524910 c.976-14C>G NM_000338.2 SLC3A1 Chr2:44528119 c.1012-23C>G NM_000341.3 https://blueprintgenetics.com/ SLC4A1 Chr17:42340296 c.-62G>A NM_000342.3 rs387906565 SLC7A9 Chr19:33334874 c.978-17G>A NM_014270.4 rs45628833 Test Strengths The strengths of this test include: CAP accredited laboratory CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance Careful construction of clinically effective and scientifically justified gene panels Some of the panels include the whole mitochondrial genome (please see the Panel Content section) Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level Our publicly available analytic validation demonstrating complete details of test performance ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section) Our rigorous variant classification scheme Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data Our comprehensive clinical statements Test Limitations Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above). This test does not d etect the following: Complex inversions Gene conversions Balanced translocations Some of the panels include the whole mitochondrial genome (please see the Panel Content section) Repeat expansion disorders unless specifically mentioned Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel). This test may not reliably detect the following: Low level mosaicism in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability) Stretches of mononucleotide repeats Low level heteroplasmy in mtDNA (>90% are detected at 5% level) Indels larger than 50bp Single exon deletions or duplications Variants within pseudogene regions/duplicated segments Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis. The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics. For additional information, please refer to the Test performance section and see our Analytic Validation. https://blueprintgenetics.com/ Test Performance The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience. Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see
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