Hereditary Spastic Paraplegia Comprehensive Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
2673 ABCD1 81405,81479 Order Options and Pricing
ACO2 81479,81479
ADAR 81479,81479
AFG3L2 81479,81479
ALDH18A1 81479,81479
ALS2 81479,81479
AMPD2 81479,81479
AP4B1 81479,81479
AP4E1 81479,81479
AP4M1 81479,81479
AP4S1 81479,81479
AP5Z1 81479,81479
ARG1 81479,81479
ARL6IP1 81479,81479
ARSI 81479,81479
ATL1 81406,81479
ATL3 81479,81479
ATP13A2 81479,81479
ATP2B4 81479,81479
ATRX 81479,81479
B4GALNT1 81479,81479
BICD2 81479,81479
BSCL2 81406,81479
C19orf12 81479,81479
CAPN1 81479,81479
CCT5 81479,81479
CPT1C 81479,81479
CYP27A1 81479,81479
CYP2U1 81479,81479
CYP7B1 81479,81479
DARS1 81479,81479
DDHD1 81479,81479
DDHD2 81479,81479
DSTYK 81479,81479
ENTPD1 81479,81479
ERLIN1 81479,81479
ERLIN2 81479,81479
EXOSC3 81479,81479
FA2H 81479,81479
FARS2 81479,81479
FLRT1 81479,81479
GAD1 81479,81479
GBA2 81479,81479
GCH1 81405,81479
GJC2 81479,81479
HACE1 81479,81479
HSPD1 81479,81479
IBA57 81479,81479
IFIH1 81479,81479
ITPR1 81479,81479
KDM5C 81407,81479
KIDINS220 81479,81479
KIF1A 81479,81479
KIF1C 81479,81479
KIF5A 81479,81479
L1CAM 81407,81479
LYST 81479,81479
MAG 81479,81479
MARS1 81479,81479
MFN2 81406,81479
MTRFR 81479,81479
NARS2 81479,81479
NIPA1 81404,81479
NT5C2 81479,81479
PGAP1 81479,81479
PLA2G6 81479,81479
PLP1 81405,81404
PNPLA6 81479,81479
POLR3A 81479,81479
RAB3GAP2 81479,81479
REEP1 81405,81479
REEP2 81479,81479
RNF170 81479,81479
RTN2 81479,81479
SACS 81479,81479
SARS2 81479,81479
SERAC1 81479,81479
SETX 81406,81479
SLC16A2 81405,81404
SLC25A15 81479,81479
SLC33A1 81479,81479
SPART 81479,81479
SPAST 81406,81405
SPG11 81407,81479
SPG21 81479,81479
SPG7 81406,81405
SPTAN1 81479,81479
TECPR2 81479,81479
TFG 81479,81479
TRPV4 81479,81479
TUBB4A 81479,81479
UBAP1 81479,81479
UCHL1 81479,81479
UNC80 81479,81479
USP8 81479,81479
VAMP1 81479,81479
VCP 81479,81479
VPS37A 81479,81479
WASHC5 81407,81479
WDR48 81479,81479
ZFR 81479,81479
ZFYVE26 81479,81479
ZFYVE27 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
2673Genes x (103)81479 81404, 81405, 81406, 81407, 81479 $1310 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Hereditary spastic paraplegia (HSP) is a group of clinically and genetically diverse diseases, characterized by bilateral lower extremity spasticity (rigid muscles) and weakness (Fink. 2014. PubMed ID: 25192507; Hensiek et al. 2015. PubMed ID: 25480570; Hedera. 2018. PubMed ID: 20301682). HSP is classified as “pure” or “uncomplicated” when symptoms are confined to lower extremity spasticity and weakness and hypertonic urinary bladder. In contrast, HSP is classified as “complex” or “complicated” if the impairments in the lower limbs are also accompanied by other systemic or neurologic abnormalities such as seizures, ataxia, intellectual disability, dementia, peripheral neuropathy, and vision and hearing impairment (Fink. 2014. PubMed ID: 20301682; Hedera. 2018. PubMed ID: 20301682). The incidence of all forms of HSP is estimated to be less than one in 10,000 individuals or 0.01% (Hensiek et al. 2015. PubMed ID: 25480570).

Symptoms of the disease may begin at any age, with early onset HSP beginning in early childhood and often resembling spastic diplegic cerebral palsy and late onset HSP beginning later in childhood or early adulthood (Fink. 2014. PubMed ID: 25192507; Hedera. 2018. PubMed ID: 20301682). In addition to variation in the age of onset, the severity and rate of progression are highly variable among different subtypes of complex HSPs, and even within a specific subtype (Tesson et al. 2015. PubMed ID: 25758904).

Advantages of genetic testing for HSP include confirmation of diagnosis, identification of other health risks associated with complicated HSP, allowing for targeted testing of other family members, and assistance with reproductive planning (Hedera. 2018. PubMed ID: 20301682). 

Genetics

To date, more than 90 genetic loci and over 70 genes have been shown to be involved in HSP (Tesson et al. 2015. PubMed ID: 25758904; de Souza et al. 2017. PubMed ID: 27271711). HSP may be inherited in an autosomal dominant (AD) (75% to 80% of cases), autosomal recessive (AR) manner (25% to 30%); or X-linked (XL) (1% to 2%) manner (Hensiek et al. 2015. PubMed ID: 25480570; Hedera. 2018. PubMed ID: 20301682). The genotype-phenotype correlation is poor, and some genes are associated with both complex and pure HSP (Fink. 2013. PubMed ID: 23897027). 

See individual gene test descriptions for information on molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

This multi-gene panel analyzes 103 genes, including the most common genetic causes of Hereditary Spastic Paraplegia (HSP), such as SPAST, ATL1, SPG11, CYP7B1, KIF5A, REEP1, PGN, ZFYVE26 and L1CAM. These genes account for approximately 63% of affected individuals (Hedera. 2018. PubMed ID: 20301682). To increase the clinical sensitivity of the test, we also include genes identified more recently; however, each of these genes accounts for a small proportion of individuals with spastic paraplegia.

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.9% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing.

For technical reasons, exon 8 of the ABCD1 gene is not currently included in this panel.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Individuals with symptoms consistent with spastic paraplegia are candidates for this test. Because this panel covers genes with dominant, recessive, and X-linked inheritance patterns, this test may be particularly helpful if the inheritance pattern is unclear based on the patient’s family history.

Diseases

Name Inheritance OMIM ID
Adrenoleukodystrophy XL 300100
Allan-Herndon-Dudley Syndrome XL 300523
Amyotrophic Lateral Sclerosis Type 2 AR 205100
Arginase Deficiency AR 207800
ATR-X Syndrome XL 301040
Cerebral Palsy, Spastic Quadriplegic, 1 AR 603513
Charcot-Marie-Tooth Disease Type 2C AD 606071
Chediak-Higashi Syndrome AR 214500
Combined Oxidative Phosphorylation Deficiency 7 AR 613559
Dystonia 4, Torsion AD 128101
Dystonia 5, Dopa-Responsive Type AR 128230
Hypomyelination with Brainstem and Spinal Cord Involvement and Leg Spasticity AR 615281
Hypotonia, Infantile, with Psychomotor Retardation and Characteristic Facies 2 AR 616801
Infantile-Onset Ascending Hereditary Spastic Paralysis 607225
MASA Syndrome XL 303350
Mast Syndrome AR 248900
Mental Retardation, X-Linked, Syndromic, Claes-Jensen Type XL 300534
Neurodegeneration With Brain Iron Accumulation 4 AR 614298
Neuropathy, Hereditary Sensory, With Spastic Paraplegia AR 256840
Pontocerebellar Hypoplasia Type 1B AR 614678
Scapuloperoneal Spinal Muscular Atrophy AD 181405
Spastic ataxia 1, autosomal dominant AD 108600
Spastic Ataxia 2, Autosomal Recessive 611302
Spastic ataxia 5, autosomal recessive AR 614487
Spastic Ataxia Charlevoix-Saguenay Type AR 270550
Spastic Paraplegia 10 AD 604187
Spastic Paraplegia 11 AR 604360
Spastic Paraplegia 12 AD 604805
Spastic Paraplegia 13 AD 605280
Spastic Paraplegia 15 AR 270700
Spastic Paraplegia 17 AD 270685
Spastic Paraplegia 18 AR 611225
Spastic Paraplegia 2 XL 312920
Spastic Paraplegia 23 AD 270750
Spastic Paraplegia 26 AR 609195
Spastic Paraplegia 28 AR 609340
Spastic Paraplegia 3 AD 182600
Spastic Paraplegia 30 AR 610357
Spastic Paraplegia 31 AD 610250
Spastic Paraplegia 33 AD 610244
Spastic paraplegia 35 AR 612319
Spastic Paraplegia 39 AR 612020
Spastic Paraplegia 4 AD 182601
Spastic Paraplegia 42 AD 612539
Spastic Paraplegia 43 AR 615043
Spastic Paraplegia 44 AR 613206
Spastic Paraplegia 45 AR 613162
Spastic Paraplegia 46 AR 614409
Spastic Paraplegia 47 AR 614066
Spastic Paraplegia 48 AR 613647
Spastic Paraplegia 49 AR 615031
Spastic Paraplegia 50 AR 612936
Spastic Paraplegia 51 AR 613744
Spastic Paraplegia 52 AR 614067
Spastic Paraplegia 53 AR 614898
Spastic Paraplegia 54 AR 615033
Spastic Paraplegia 55 AR 615035
Spastic Paraplegia 56 AR 615030
Spastic Paraplegia 57 AR 615658
Spastic Paraplegia 5A AR 270800
Spastic Paraplegia 6 AD 600363
Spastic Paraplegia 61 AR 615685
Spastic Paraplegia 62 AR 615681
Spastic Paraplegia 63 AR 615686
Spastic Paraplegia 64 AR 615683
Spastic Paraplegia 7 AD,AR 607259
Spastic Paraplegia 72 AD,AR 615625
Spastic Paraplegia 73 AD 616282
Spastic Paraplegia 74 AR 616451
Spastic Paraplegia 75 AR 616680
Spastic Paraplegia 76 AR 616907
Spastic Paraplegia 77 AR 617046
Spastic Paraplegia 78 AR 617225
Spastic Paraplegia 79 AR 615491
Spastic Paraplegia 8 AD 603563
Spastic paraplegia 80, autosomal dominant AD 618418
Spastic Paraplegia 9A AD 601162
Spastic Paraplegia 9B AR 616586
Spastic Paraplegia and Psychomotor Retardation with or without Seizures AR 616756
Spastic Paraplegia, Intellectual Disability, Nystagmus, and Obesity AD 617296
Spinocerebellar Ataxia 15 AD 606658
Spinocerebellar ataxia 29, congenital nonprogressive AD 117360
Spinocerebellar Ataxia Autosomal Recessive 1 AR 606002
Troyer Syndrome AR 275900

Related Test

Name
PGxome®

Citations

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

Disease Resources

Spastic Paraplegia Foundation, Inc. (https://sp-foundation.org/) 

NIH/National Institute of Neurological Disorders and Stroke (https://www.ninds.nih.gov/) 

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ORDER OPTIONS

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2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

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