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Spastic Paraplegia 48 via the AP5Z1 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
AP5Z1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
5279AP5Z181479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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 48 (SPG48) is a type of hereditary spastic paraplegia (HSP) characterized by spasticity and weakness of the lower limbs resulting in walking abnormalities. Additional features may include ataxia, sensory and motor neuropathy, urinary incontinence, mild cognitive impairment and parkinsonism (Hirst et al. 2015). SPG48 has been reported in a small number of patients. Most patients have disease onset in their 50s or 60s, although early onset has been reported in one patient (Slabicki et al. 2010; Pensato et al. 2014; Hirst et al. 2015).


The transmission pattern of SPG48 in the reported families is consistent with autosomal recessive (AR) inheritance. This disorder is caused by pathogenic variants in AP5Z1 gene (previously known as KIAA0415) (Slabicki et al. 2010). To date, different types of pathogenic variants (missense, nonsense and small deletions resulting in frameshifts) have been found in this gene to cause SPG48 (Human Gene Mutation Database). AP5Z1 encodes a subunit of the adaptor protein 5 complex (AP5), AP5 –Zeta, with both cytoplasmic and nuclear localization, involved in DNA damage repair (Slabicki et al. 2010). AP5Z1 might be also involved in intracellular sorting and trafficking of cargo proteins (Hirst et al. 2011).

Clinical Sensitivity - Sequencing with CNV PGxome

It is difficult to estimate the exact clinical sensitivity of this test due to the lack of large cohort studies. All the pathogenic variants in the AP5Z1 gene reported to date can be detected by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the AP5Z1 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 AP5Z1.


Official Gene Symbol OMIM ID
AP5Z1 613653
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Spastic Paraplegia 48 AR 613647


  • Hirst J. et al. 2011. Plos Biology. 9: e1001170. PubMed ID: 22022230
  • Hirst J. et al. 2015. Human Molecular Genetics. 24: 4984-96. PubMed ID: 26085577
  • Human Gene Mutation Database (Bio-base).
  • Pensato V. et al. 2014. Brain. 137: 1907-20. PubMed ID: 24833714
  • Slabicki M. et al. 2010. Plos Biology. 8: e1000408. PubMed ID: 20613862


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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