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Blueprint Genetics Spastic Paraplegia Panel

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Blueprint Genetics Spastic Paraplegia Panel Spastic Paraplegia Panel Test code: NE0501 Is a 75 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion of spastic paraplegia. About Spastic Paraplegia Spastic paraplegia is a group of clinically and genetically heterogeneous neurodegenerative disorders characterized by lower extremity spasticity and weakness. If symptoms begin in early childhood, they may be non-progressive and resemble spastic diplegic cerebral palsy. If symptoms begin later, they usually progress slowly and steadily. Spastic paraplegia is classified clinically as non-syndromic (uncomplicated) or syndromic (complicated). Non-syndromic spastic paraplegias are characterized by slowly progressive spasticity and weakness of the lower extremity, often associated with hypertonic urinary disturbances, mild reduction of lower extremity vibration sense and, occasionally, of joint position sensation. Syndromic forms of spastic paraplegia are characterized by the presence of additional neurological or non-neurological features. The prevalence of HSP is estimated to be 1-9/100,000 (GeneReviews NBK1509). Availability 4 weeks Gene Set Description Genes in the Spastic Paraplegia Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ABCD1* Adrenoleukodystrophy XL 95 663 AFG3L2* Spastic ataxia, Spinocerebellar ataxia AD/AR 22 40 ALDH18A1 Spastic paraplegia, Cutis laxa AD/AR 22 30 ALS2 Amyotrophic lateral sclerosis, Spastic paralysis AR 33 68 AP4B1 Spastic paraplegia 47, autosomal recessive AR 17 18 AP4E1 Stuttering, familial persistent, 1, Spastic paraplegia 51, autosomal recessive AD/AR 7 15 AP4M1 Spastic paraplegia 50, autosomal recessive AR 16 13 AP4S1* Spastic paraplegia 52, autosomal recessive AR 9 8 AP5Z1 Spastic paraplegia 48, autosomal recessive AR 11 14 ARG1 Hyperargininemia AR 28 54 ARL6IP1 Spastic paraplegia 61 AR 1 4 ATAD3A* Harel-Yoon syndrome AD/AR 4 17 ATL1 Spastic paraplegia, Neuropathy, hereditary sensory AD 29 84 B4GALNT1 Spastic paraplegia AR 7 13 https://blueprintgenetics.com/ BSCL2 Lipodystrophy, congenital generalized, Encephalopathy, progressive, AD/AR 34 50 Neuropathy, distal hereditary motor, type VA, Charcot-Marie-Tooth disease type 2, Silver syndrome, Silver spastic paraplegia syndrome, Spastic paraplegia 17 BTD Biotinidase deficiency AR 170 247 C12ORF65 Spastic paraplegia, Combined oxidative phosphorylation deficiency AR 10 11 C19ORF12 Spastic Paraplegia, Neurodegeneration with brain iron accumulation AR 15 37 CACNA1G Spinocerebellar ataxia 42 8 11 CAPN1 Spastic paraplegia 76, autosomal recessive AR 6 16 COASY Neurodegeneration with brain iron accumulation 6 AR 3 3 CTNNB1 Exudative vitreoretinopathy 7, Mental retardation, autosomal dominant 19 AD 90 51 CYP27A1 Cerebrotendinous xanthomatosis AR 69 110 CYP2U1 Spastic paraplegia 56, autosomal recessive AR 14 19 CYP7B1 Bile acid synthesis defect, Spastic paraplegia 5A, autosomal recessive AR 18 60 DARS Hypomyelination with brainstem and spinal cord involvement and leg AR 11 17 spasticity DDHD1 Spastic paraplegia AR 5 11 DDHD2 Spastic paraplegia AR 18 19 ERLIN2 Spastic paraplegia 18, autosomal recessive AR 7 13 FA2H Spastic paraplegia AR 18 51 FARS2 Combined oxidative phosphorylation deficiency 14, Spastic paraplegia 77, AR 17 20 autosomal recessive FXN* Friedreich ataxia AR 13 63 GALC Krabbe disease AR 107 243 GBA2 Cerebellar ataxia with spasticity AR 11 22 GBE1 Glycogen storage disease AR 36 70 GCH1 Dopa-Responsive Dystonia Hyperphenylalaninemia, BH4-deficient, GTP AD/AR 48 240 Cyclohydrolase 1-Deficient Dopa-Responsive Dystonia GJC2 Spastic paraplegia, Lymphedema, hereditary, Leukodystrophy, AD/AR 26 57 hypomyelinating GPT2 Mental retardation, autosomal recessive 49, Microcephaly, Spastic AR 5 7 paraplegia HACE1 Spastic paraplegia and psychomotor retardation with or without seizures AR 13 13 HSPD1* Spastic paraplegia, Leukodystrophy, hypomyelinating AD/AR 5 5 https://blueprintgenetics.com/ IBA57 Multiple mitochondrial dysfunctions syndrome 3, Spastic paraplegia 74, AR 14 23 autosomal recessive IRF2BPL Neurodevelopmental disorder with hypotonia, seizures, and absent AD 9 2 language KDM5C Mental retardation, syndromic, Claes-Jensen XL 47 55 KIAA0196 Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome) AD/AR 15 18 KIDINS220 Spastic paraplegia, intellectual disability, nystagmus, and obesity (SINO) AD/AR 4 8 KIF1A Spastic paraplegia, Neuropathy, hereditary sensory, Mental retardation AD/AR 63 42 KIF5A Spastic paraplegia AD 18 62 L1CAM Mental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) XL 80 292 syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesis L2HGDH L-2-hydroxyglutaric aciduria AR 15 79 MARS2 Combined oxidative phosphorylation deficiency AR 8 5 NIPA1 Spastic paraplegia AD 5 16 NKX6-2 Spastic ataxia 8, autosomal recessive, with hypomyelinating AR 4 8 leukodystrophy NT5C2 Spastic paraplegia 45 AR 8 7 PAH Hyperphenylalaninemia, non-PKU mild, Phenylketonuria AR 294 966 PLP1 Spastic paraplegia, Pelizaeus-Merzbacher disease XL 60 348 PNPLA6 Laurence-Moon syndrome, Boucher-Neuhauser syndrome, Spastic AR 26 58 paraplegia 39 RARS Leukodystrophy, hypomyelinating 9 AR 12 11 REEP1 Spastic paraplegia, Distal hereditary motor neuronopathy AD 16 60 RTN2 Spastic paraplegia 12, autosomal dominant AD 4 5 SACS Spastic ataxia, Charlevoix-Saguenay AR 254 262 SETX Ataxia with oculomotor apraxia, Amyotrophic lateral sclerosis, juvenile, AD/AR 36 210 Spinocerebellar ataxia SLC16A2 Allan-Herndon-Dudley syndrome XL 39 84 SLC1A4 Spastic tetraplegia, thin corpus callosum, and progressive microcephaly AR 4 8 SLC25A15* Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome AR 24 36 SLC33A1* Congenital cataracts, hearing loss, and neurodegeneration, Spastic AD/AR 6 7 paraplegia 42, autosomal dominant SPAST Spastic paraplegia AD 193 723 https://blueprintgenetics.com/ SPG11 Spastic paraplegia, Amyotrophic lateral sclerosis, Charcot-Marie-Tooth AR 162 274 disease SPG20 Spastic paraplegia (Troyer syndrome) AR 9 7 SPG7 Spastic paraplegia AR 69 111 SPR Dystonia, Dopa-responsive, due to sepiapterin reductase deficiency AR 12 23 TECPR2 Spastic paraplegia 49, autosomal recessive AR 9 6 TFG Spastic paraplegia, Hereditary motor and sensory neuropathy, proximal AR 4 7 TH Segawa syndrome, autosomal recessive AR 44 71 UBAP1 Spastic paraplegia AD 1 ZFYVE26 Spastic paraplegia 15 AR 63 39 *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. 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 HGVS RefSeq RS-number location HG19 ARG1 Chr6:131901748 c.306-611T>C NM_000045.3 BSCL2 Chr11:62470032 c.405-11A>G NM_001122955.3 BTD Chr3:15683399 c.310-15delT NM_000060.2 rs587783008 BTD Chr3:15687154 c.*159G>A NM_000060.2 rs530872564 GALC Chr14:88401064 c.*12G>A NM_000153.3 rs372641636 GALC Chr14:88459574 c.-66G>C NM_000153.3 rs146439771 GALC Chr14:88459575 c.-67T>G NM_000153.3 rs571945132 GALC Chr14:88459917 c.-74T>A NM_001201402.1 GALC Chr14:88459971 c.-128C>T NM_001201402.1 rs181956126 GBE1 Chr3:81542964 c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATGACAGGT NM_000158.3 rs869320698 GCH1 Chr14:55369403 c.-22C>T NM_000161.2 GJC2 Chr1:228337558 c.-170A>G NM_020435.3 https://blueprintgenetics.com/ GJC2 Chr1:228337561 c.-167A>G NM_020435.3 GJC2 Chr1:228337709 c.-20+1G>C NM_020435.3 L1CAM ChrX:153128846 c.3531-12G>A NM_000425.4 L1CAM ChrX:153131293 c.2432-19A>C NM_000425.4 L1CAM ChrX:153133652 c.1704-75G>T NM_000425.4 L1CAM ChrX:153133926 c.1547-14delC NM_000425.4 L1CAM ChrX:153136500 c.523+12C>T NM_000425.4 L2HGDH Chr14:50735527 c.906+354G>A NM_024884.2 PAH Chr12:103232809 c.*144A>G NM_000277.1 rs375319584 PAH Chr12:103237404 c.1199+20G>C NM_000277.1 rs62509018 PAH Chr12:103237407 c.1199+17G>A NM_000277.1 rs62508613 PAH Chr12:103237568 c.1066-11G>A NM_000277.1 rs5030855 PAH Chr12:103237568 c.1066-12delT NM_000277.1 PAH Chr12:103237570 c.1066-13T>G NM_000277.1 PAH Chr12:103237571 c.1066-14C>G NM_000277.1 rs62507334 PAH Chr12:103238075 c.1065+39G>T NM_000277.1 rs62510582 PAH Chr12:103260355 c.509+15_509+18delCTTG NM_000277.1 rs1335303703 PAH Chr12:103288709 c.169-13T>G NM_000277.1 rs62507341 PLP1 ChrX:103031997 c.4+78_4+85delGGGGGTTC NM_000533.3 PLP1 ChrX:103041680 c.453+28_453+46delTAACAAGGGGTGGGGGAAA NM_000533.3 PLP1 ChrX:103042405 c.454-322G>A NM_000533.3 PLP1 ChrX:103042413 c.454-314T>A/G NM_000533.3 PLP1 ChrX:103042413 c.454-314T>A NM_000533.3
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