Spastic Paraplegia 5A via the CYP7B1 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 15239 | CYP7B1 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
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 5A (SPG5A) is a type of hereditary spastic paraplegia (HSP) with a wide phenotypic spectrum (Lo Giudice et al. 2014). Some SPG5A patients have “pure” spastic paraplegia, i.e., the symptoms are primarily limited to lower limb weakness and spasticity. While in other patients, the clinical feature is complicated by distal muscle atrophy, axonal neuropathy, cerebellar ataxia, and white matter abnormalities on brain MRI (Biancheri et al. 2009; Criscuolo et al. 2009; Arnoldi et al. 2012). The age at onset of SPG5A ranges from 4-47 years (Wilkinson et al. 2003; Goizet et al. 2009).
Genetics
SPG5A is inherited in an autosomal recessive (AR) manner. This disorder makes up approximately 5%-10% of AR HSP (Arnoldi et al. 2012; Denora et al. 2013; Lo Giudice et al. 2014). SPG5A is caused by pathogenic variants in the CYP7B1 gene. Pathogenic variants in this gene include missense, nonsense, splicing and frame shift variants (Human Gene Mutation Database).
CYP7B1 encodes cytochrome P450 oxysterol 7-alpha-hydroxylase (CYP7B1), an enzyme that regulates the cholesterol catabolic pathway to convert cholesterol to bile acids (Tsaousidou et al. 2008). The abnormal cholesterol metabolism in the brain is believed to be involved in the pathogenicity of SPG5A (Mignarri et al. 2014).
SPG3A is allelic with another autosomal recessive disorder, congenital bile acid synthesis defect 3. To date, two homozygous pathogenic variants have been identified to cause severe cholestasis (Setchell et al. 1998; Ueki et al. 2008).
Clinical Sensitivity - Sequencing with CNV PG-Select
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 CYP7B1 can be detected by sequencing.
Testing Strategy
This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.
This test provides full coverage of all coding exons of the CYP7B1 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.
Indications for Test
Individuals with symptoms consistent with AR HSP and family members of patients who have known CYP7B1 pathogenic variants are candidates for this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CYP7B1.
Individuals with symptoms consistent with AR HSP and family members of patients who have known CYP7B1 pathogenic variants are candidates for this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CYP7B1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| CYP7B1 | 603711 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Bile Acid Synthesis Defect, Congenital, 3 | AR | 613812 |
| Spastic Paraplegia 5A | AR | 270800 |
Citations
- Arnoldi A. et al. 2012. Clinical Genetics. 81: 150-7. PubMed ID: 21214876
- Biancheri R. et al. 2009. Neuromuscular Disorders : Nmd. 19: 62-5. PubMed ID: 19187859
- Criscuolo C. et al. 2009. Journal of Neurology. 256: 1252-7. PubMed ID: 19363635
- Denora P.S. et al. 2013. Handbook of Clinical Neurology. 113: 1899-912. PubMed ID: 23622413
- Goizet C. et al. 2009. Brain : a Journal of Neurology. 132: 1589-600. PubMed ID: 19439420
- Human Gene Mutation Database (Bio-base).
- Lo Giudice T. et al. 2014. Experimental Neurology. 261: 518-39. PubMed ID: 24954637
- Mignarri A. et al. 2014. Journal of Neurology. 261: 617-9. PubMed ID: 24509641
- Setchell K.D. et al. 1998. The Journal of Clinical Investigation. 102: 1690-703. PubMed ID: 9802883
- Tsaousidou M.K. et al. 2008. American Journal of Human Genetics. 82: 510-5. PubMed ID: 18252231
- Ueki I. et al. 2008. Journal of Pediatric Gastroenterology and Nutrition. 46: 465-9. PubMed ID: 18367963
- Wilkinson P.A. et al. 2003. Neurology. 61: 235-8. PubMed ID: 12874406
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
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ORDER OPTIONS
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