Spastic Paraplegia 62 via the ERLIN1 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 4901 | ERLIN1 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Spastic Paraplegia 62 (SPG62) is a type of hereditary spastic paraplegia (HSP) that has been identified recently by whole-exome sequencing (WES) in combination with network analysis (Novarino et al. 2014). Novarino et al. (2014) reported patients from 3 consanguineous families segregating ERLIN1 pathogenic variants. Typically, this is a “pure” form of HSP, i.e., the symptoms are restricted in the lower limbs. SPG62 patients usually can walk unsupported for a short distance with abnormal gait, and have increased deep tendon reflexes. Most of them have normal brain MRIs and normal cognition.
Genetics
SPG is inherited as an autosomal recessive (AR) disorder. In 3 consanguineous families, Novarino et al. (2014) identified a nonsense (c.763C>T), a missense (c.149G>T) and a frameshift (c.862_867delACCAGG) variant in ERLIN1 (ER lipid Raft Associated 1). ERLIN1 and its paralog ERLIN2 (SPG18) regulate the endoplasmic reticulum-associated degradation (ERAD) of inositol 1,4,5-trisphosphate receptors (IP3Rs). ERLIN1/ERLIN2 also mediates cellular cholesterol homeostasis through the SREBP (sterol regulatory element binding proteins) signaling pathway (Huber et al. 2013; Pearce et al. 2009). The exact mechanism of ERLIN1-associated SPG62 is not understood.
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. All the reported pathogenic variants in ERLIN1 are detectable by sequencing.
Testing Strategy
This test provides full coverage of all coding exons of the ERLIN1 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 ERLIN1.
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 ERLIN1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| ERLIN1 | 611604 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Spastic Paraplegia 62 | AR | 615681 |
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.
- 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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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.