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Pure Hereditary Spastic Paraplegia Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
AP5Z1 81479,81479
ATL1 81406,81479
ATL3 81479,81479
ATP2B4 81479,81479
BICD2 81479,81479
CAPN1 81479,81479
CPT1C 81479,81479
CYP2U1 81479,81479
CYP7B1 81479,81479
DDHD1 81479,81479
ERLIN1 81479,81479
FARS2 81479,81479
HSPD1 81479,81479
ITPR1 81479,81479
KIF1A 81479,81479
KIF1C 81479,81479
KIF5A 81479,81479
MFN2 81406,81479
NIPA1 81404,81479
NT5C2 81479,81479
PLP1 81405,81404
POLR3A 81479,81479
REEP1 81405,81479
REEP2 81479,81479
RTN2 81479,81479
SETX 81406,81479
SLC33A1 81479,81479
SPAST 81406,81405
SPG11 81407,81479
SPG7 81406,81405
SPTAN1 81479,81479
UBAP1 81479,81479
WASHC5 81407,81479
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
2679Genes x (36)81479 81404(x2), 81405(x4), 81406(x5), 81407(x2), 81479(x59) $990 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 Custom Panel tool.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

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


Genetic Counselors


  • Greg Fischer, PhD

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 (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). Patients with pure HSP typically maintain normal function of the upper limb and have no abnormalities in speech or swallowing. In addition, pure HSP does not shorten lifespan (Hedera. 2018. PubMed ID: 20301682).

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).


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). This multi-gene panel contains causative genes solely for pure HSP as well as the ones that can cause both pure and complex HSP.

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 includes almost all the currently known causative genes for pure Hereditary Spastic Paraplegia (HSP). It is difficult to estimate the clinical sensitivity of this test due to the lack of data. Based on the frequencies of some causative genes in this panel (Hedera. 2018. PubMed ID:  20301682), we predict that this test should detect causative variants in at least 50% of patients with a pure HSP phenotype.

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 coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Individuals with symptoms consistent with pure 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 useful if the inheritance pattern is unclear based on the patient’s family history.

Related Test




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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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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View Ordering Instructions

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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