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Pantothenate Kinase-Associated Neurodegeneration (PKAN, Hallervorden-Spatz Disease) via the PANK2 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
8347 PANK2 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8347PANK281479 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

  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Pantothenate kinase-associated neurodegeneration (PKAN), also known as Hallervorden-Spatz disease, is a rare inborn error of Vitamin B5 metabolism. PKAN is also the most common type of Neurodegeneration with brain iron accumulation (NBIA) and occurs in approximately two-thirds of NBIA patients. In Classic PKAN, children typically manifest gait abnormalities around age three years and later develop progressive dystonia, dysarthria, rigidity, spasticity, hyperreflexia, extensor toe signs and retinal degeneration. In atypical PKAN, patients start their manifestation in the second and third decade of life and progress slower than classic PKAN. Hallmark features in brain MRI show excess iron accumulation in the globus pallidus as “eye of the tiger” pattern. The elevation of lactate in PKAN patients, suggesting dysfunctional mitochondrial metabolism. The biochemical markers also include increased level of pantothenate, defects in bile acid conjugation and lipid metabolism (Hayflick et al. 2003; Leoni et al. 2012; Arber et al. 2016).

Genetics

Pantothenate kinase-associated neurodegeneration (PKAN or Hallervorden-Spatz disease) is inherited in an autosomal recessive manner and caused by pathogenic variants in the PANK2 gene which encodes pantothenate kinase 2. This kinase is a rate-limiting essential regulatory enzyme in CoA biosynthesis located in the mitochondria. Pathogenic variants in PANK2 include missense, nonsense, small deletion and insertion, and splice variants, as well as large deletions in the PANK2 locus (Hayflick et al. 2003; Leoni et al 2012; Lee et al 2016; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in PANK2 account for 35%-50% of Neurodegeneration with brain iron accumulation cases (Gregory and Hayflick 2014).

Testing Strategy

This test provides full coverage of all coding exons of the PANK2 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

Candidates for this gene include patients with symptoms suspected for neurodegeneration with brain iron accumulation. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PANK2.

Gene

Official Gene Symbol OMIM ID
PANK2 606157
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Neurodegeneration With Brain Iron Accumulation 1 AR 234200

Citations

  • Arber C.E. et al. 2016. Neuropathology and Applied Neurobiology. 42: 220-41. PubMed ID: 25870938
  • Hayflick S.J. et al. 2003. The New England Journal of Medicine. 348: 33-40. PubMed ID: 12510040
  • Human Gene Mutation Database (Bio-base).
  • Lee J.H. et al. 2016. Journal of Movement Disorders. 9: 20-7. PubMed ID: 26828213
  • Leoni V. et al. 2012. Molecular Genetics and Metabolism. 105: 463-71. PubMed ID: 22221393

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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