Parkinsonism with Spasticity and Mental Retardation with Epilepsy, Hedera Type via the ATP6AP2 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 | |
|---|---|---|---|---|---|
| 9821 | ATP6AP2 | 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
Parkinsonism with spasticity, X-linked presents either as typical adult onset Parkinson’s disease or earlier onset spasticity followed by parkinsonism. The major clinical symptoms are slowly progressive Parkinsonism, cogwheel rigidity, bradykinesia, resting tremor, and masked facies. Onset is variable from 14 to 50 years. Other clinical features may include spasticity, hyperreflexia and extensor plantar response. Some patients showed a response to L-DOPA therapy (Hedera et al. 2002. PubMed ID: 11782983; Ramser et al. 2005. PubMed ID: 15746149; Korvatska et al. 2013. PubMed ID: 23595882).
Mental retardation, X-linked, syndromic, Hedera type is characterized by early infantile onset intellectual disability, generalized tonic-clonic seizures, delayed motor and speech development with variable expressivity. Other features may include Parkinsonism, bradykinesia, gait difficulties, action tremor, ideomotor aprasia and cerebral atrophy (Korvatska et al. 2013. PubMed ID: 23595882; Piton et al. 2013. PubMed ID: 23871722).
Female patients have not been reported to date (Hedera et al. 2002. PubMed ID: 11782983; Ramser et al. 2005. PubMed ID: 15746149; Korvatska et al. 2013. PubMed ID: 23595882).
Genetics
Both Parkinsonism with spasticity, X-linked disorder and Mental retardation, X-linked, syndromic, Hedera type are inherited in an X-linked recessive manner and are caused by pathogenic variants in the ATP6AP2 (Korvatska et al. 2013. PubMed ID: 23595882; Piton et al. 2013. PubMed ID: 23871722). ATP6AP2 encodes ATPase, H+ transporting, lysosomal, accessory protein 2, which is required for lysosomal degradative functions and autophagy, a pathway frequently affected in Parkinson’s disease. Reported pathogenic variants in ATP6AP2 include splicing variants and one large deletion. The large deletion was reported to be causative for intellectual disability (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
For the ATP6AP2 gene, clinical sensitivity in a large cohort of patients with either Parkinsonism with spasticity or mental retardation with epilepsy relevant phenotypes is unavailable in the literature. Analytical sensitivity should be high.
Testing Strategy
This test provides full coverage of all coding exons of the ATP6AP2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
ATP6AP2 sequencing is recommended for patients who are suspected to have both Parkinsonism with spasticity, X-linked disorder or Mental retardation, X-linked, syndromic, Hedera type. Targeted Sanger sequencing is available for the family members of patients with ATP6AP2 pathogenic variants. Prenatal testing is possible if the genetic diagnosis has been firmly established in an affected family member.
ATP6AP2 sequencing is recommended for patients who are suspected to have both Parkinsonism with spasticity, X-linked disorder or Mental retardation, X-linked, syndromic, Hedera type. Targeted Sanger sequencing is available for the family members of patients with ATP6AP2 pathogenic variants. Prenatal testing is possible if the genetic diagnosis has been firmly established in an affected family member.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| ATP6AP2 | 300556 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Mental Retardation, X-Linked, Syndromic, Hedera Type | XL | 300423 |
| Parkinsonism with Spasticity, X-Linked | XL | 300911 |
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
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ORDER OPTIONS
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2) Select Additional Test Options
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