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Spastic Paraplegia 76 via the CAPN1 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
CAPN1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
10063CAPN181479 81479,81479 $990 Order Options and Pricing

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

Spastic paraplegia 76 (SPG76) is a type of hereditary spastic paraplegia (HSP) characterized by young-adult onset of progressive spasticity of the lower limbs resulting in walking difficulties. Most SPG76 patients variably presented upper limb involvement, dysarthria, ataxia and sensory axonal neuropathy (Gan-Or et al. 2016. PubMed ID: 27153400; Wang et al. 2016. PubMed ID: 27320912). In a few cases, mild-to moderate cerebellar atrophy has also been shown on brain MRI (Wang et al. 2016. PubMed ID: 27320912). In addition to the adult-onset complicated form of HSP, a congenital-onset pure form of HSP has been reported recently in a SPG76 patient (Travaglini et al. 2017. PubMed ID: 28566166).


SPG76 is inherited in an autosomal recessive (AR) manner. Homozygous or compound heterozygous pathogenic variants in the CAPN1 gene have been reported to cause SPG76 (Gan-Or et al. 2016. PubMed ID: 27153400; Wang et al. 2016. PubMed ID: 27320912; Travaglini et al. 2017. PubMed ID: 28566166). To date, different types of pathogenic variants (missense, nonsense, splicing and small frameshift deletions/duplications) have been identified in SPG76 patients (Human Gene Mutation Database).

CAPN1 encodes for Calpain 1, a type of calcium-dependent non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in signal transduction and cytoskeletal remodeling (Ohno et al. 1990. PubMed ID: 2209092). Previous studies demonstrated that the loss-of-function of CAPN1 is the cause of this disorder (Gan-Or et al. 2016. PubMed ID: 27153400; Wang et al. 2016. PubMed ID: 27320912).

Clinical Sensitivity - Sequencing with CNV PGxome

It is difficult to estimate the clinical sensitivity of this test due to the lack of large cohort studies. Pathogenic variants in CAPN1 gene appear to be a rare cause of spastic paraplegia. All the known pathogenic variants in this gene can be detected by this test.

Testing Strategy

This test provides full coverage of all coding exons of the CAPN1 gene 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. 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

Patients with symptoms consistent with AR HSP may consider this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CAPN1.


Official Gene Symbol OMIM ID
CAPN1 114220
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Spastic Paraplegia 76 AR 616907


  • Gan-Or et al. 2016. PubMed ID: 27153400
  • Human Gene Mutation Database (Bio-base).
  • Ohno et al. 1990 PubMed ID: 2209092
  • Travaglini et al. 2017 PubMed ID: 28566166
  • Wang et al. 2016 PubMed ID: 27320912


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

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View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

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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