Spastic Paraplegia Panel

Last modified: Feb 15, 2019

Summary

  • Is a 60 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of spastic paraplegia.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

4 weeks

Number of genes

60

Test code

NE0501

Panel size

Large

CPT codes

SEQ 81479
DEL/DUP 81479

Summary

The Blueprint Genetics Spastic Paraplegia Panel (test code NE0501):

ICD codes

Commonly used ICD-10 code(s) when ordering the Spastic Paraplegia Panel

ICD-10 Disease
G11.4 Spastic paraplegia

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

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).

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
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 AR 7 15
AP4M1 Spastic paraplegia 50, autosomal recessive AR 16 13
AP4S1* Spastic paraplegia 52, autosomal recessive AR 9 8
ARG1 Hyperargininemia AR 28 54
ATAD3A* Harel-Yoon syndrome AD/AR 4 17
ATL1 Spastic paraplegia, Neuropathy, hereditary sensory AD 29 84
B4GALNT1 Spastic paraplegia AR 7 13
BSCL2 Lipodystrophy, congenital generalized, Encephalopathy, progressive, Neuropathy, distal hereditary motor, type VA, Charcot-Marie-Tooth disease type 2, Silver syndrome, Silver spastic paraplegia syndrome, Spastic paraplegia 17 AR 34 50
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
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 spasticity AR 11 17
DDHD1 Spastic paraplegia AR 5 11
DDHD2 Spastic paraplegia AR 18 19
FA2H Spastic paraplegia AR 18 51
FARS2 Combined oxidative phosphorylation deficiency 14, Spastic paraplegia 77, autosomal recessive AR 17 20
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 Cyclohydrolase 1-Deficient Dopa-Responsive Dystonia AD/AR 48 240
GJC2 Spastic paraplegia, Lymphedema, hereditary, Leukodystrophy, hypomyelinating AD/AR 26 57
HACE1 Spastic paraplegia and psychomotor retardation with or without seizures AR 13 13
HSPD1* Spastic paraplegia, Leukodystrophy, hypomyelinating AD/AR 5 5
IBA57 Multiple mitochondrial dysfunctions syndrome 3, Spastic paraplegia 74, autosomal recessive AR 14 23
KDM5C Mental retardation, syndromic, Claes-Jensen XL 47 55
KIAA0196 Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome) AD/AR 15 18
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) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesis XL 80 292
L2HGDH L-2-hydroxyglutaric aciduria AR 15 79
MARS2 Combined oxidative phosphorylation deficiency AR 8 5
NIPA1 Spastic paraplegia AD 5 16
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 paraplegia 39 AR 26 58
RARS Leukodystrophy, hypomyelinating 9 AR 12 11
REEP1 Spastic paraplegia, Distal hereditary motor neuronopathy AD 16 60
SACS Spastic ataxia, Charlevoix-Saguenay AR 254 262
SETX Ataxia with oculomotor apraxia, Amyotrophic lateral sclerosis, juvenile, Spinocerebellar ataxia AD/AR 36 210
SLC16A2 Allan-Herndon-Dudley syndrome XL 39 84
SLC25A15* Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome AR 24 36
SLC33A1* Congenital cataracts, hearing loss, and neurodegeneration, Spastic paraplegia 42, autosomal dominant AD/AR 6 7
SPAST Spastic paraplegia AD 193 723
SPG11 Spastic paraplegia, Amyotrophic lateral sclerosis, Charcot-Marie-Tooth disease AR 162 274
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
TH Segawa syndrome, autosomal recessive AR 44 71
ZFYVE26 Spastic paraplegia 15 AR 63 39

* Some, or all, of the gene is 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).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), 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 Orphanet databases.

Non-coding variants covered by Spastic Paraplegia Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ARG1 Chr6:131901748 c.306-611T>C NM_000045.3
BSCL2 Chr11:62470032 c.405-11A>G NM_001122955.3
BTD Chr3:15687154 c.*159G>A NM_000060.2 rs530872564
GALC Chr14:88459917 c.-74T>A NM_001201402.1
GJC2 Chr1:228337558 c.-170A>G NM_020435.3
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: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 Chr12:103237568 c.1066-11G>A NM_000277.1 rs5030855
PAH Chr12:103237570 c.1066-13T>G NM_000277.1
PAH Chr12:103237571 c.1066-14C>G NM_000277.1 rs62507334
PAH Chr12:103288709 c.169-13T>G NM_000277.1 rs62507341
PLP1 ChrX:103042405 c.454-322G>A NM_000533.3
PLP1 ChrX:103042413 c.454-314T>A/G NM_000533.3
SPR Chr2:73114549 c.-13G>A NM_003124.4 rs750423023
TH Chr11:2187017 c.1198-24T>A NM_199292.2
TH Chr11:2193085 c.-69T>A NM_199292.2
TH Chr11:2193086 c.-70G>A NM_199292.2
TH Chr11:2193087 c.-71C>T NM_199292.2 rs549435434

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • 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
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG 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 detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • 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 (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

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.

The Blueprint Genetics spastic paraplegia panel covers classical genes associated with spastic paraplegia. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling the following criteria are not Sanger confirmed: the variant quality score is above the internal threshold for a true positive call, and visual check-up of the variant at IGV is in-line with the variant call. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.