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Spastic Paraplegia 61 via the ARL6IP1 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
4347 ARL6IP1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4347ARL6IP181479 81479,81479 $890 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 backbone).

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

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

Spastic Paraplegia 61 (SPG61) is a type of hereditary spastic paraplegia (HSP). It has been described recently in a highly consanguineous family by whole-exome sequencing (WES) in combination with network analysis (Novarino et al. 2014). Based on phenotypic features described in this study, the affected individuals present with difficulty in walking and a scissor gait. The age of onset is about 14 months. The patients also have spasticity with loss of terminal digits as well as diffuse motor and sensory polyneuropathy mainly affected lower limbs. Cognition is normal in the patients (Novarino et al. 2014).

Genetics

SPG61 is inherited as an autosomal recessive (AR) disorder. Novarino et al identified a homozygous frameshift variant in the ARL6IP1 gene, designated c.576_579delAAAC, which is predicted to result in premature protein termination (p.K193Ffs36X) (Novarino et al. 2014). ARL6IP1 (ADP-ribosylation factor-like 6 interacting protein 1) encodes a tetraspan membrane protein, which contains highly conserved hydrophobic domains implicated in the ER (endoplasmic reticulum) formation and mitochondrial network organization (Yamamoto et al. 2014; Fowler et al. 2016).

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. The only reported pathogenic variant, c.576_579delAAAC, is detectable by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the ARL6IP1 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 clinical symptoms consistent with autosomal recessive HSP may consider this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ARL6IP1.

Gene

Official Gene Symbol OMIM ID
ARL6IP1 607669
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Spastic Paraplegia 61 AR 615685

Citations

  • Fowler P.C. et al. 2016. Human Molecular Genetics. PubMed ID: 27170313
  • Novarino G. et al. 2014. Science. 343: 506-11. PubMed ID: 24482476
  • Yamamoto Y. et al. 2014. The Biochemical Journal. 458: 69-79. PubMed ID: 24262037

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.
  • 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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

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

No Additional Test Options are available for this test.

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