Idiopathic Basal Ganglia Calcification Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
10171 PDGFB 81479,81479 Order Options and Pricing
PDGFRB 81479,81479
SLC20A2 81479,81479
XPR1 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10171Genes x (4)81479 81479 $890 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View 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

Clinical Features and Genetics

Clinical Features

Idiopathic Basal Ganglia Calcification (IBGC), also known as Fahr’s syndrome, is a neurological disorder characterized by abnormal deposits of calcium in areas of the brain that control movement. The radiological characteristics of IBGC consist of bilateral and symmetrical calcification of the basal ganglia. Additional areas of the brain may also be affected. IBGC is clinically heterogeneous. Symptoms usually begin during the fourth and fifth decades of life. Childhood and adolescent onset have also been reported. Movement disorders in the form of dystonia, tremor and chorea are the initial and most common clinical manifestations of IBGC. As the disease progresses, neurological and neuropsychiatric abnormalities are detected and include seizures, spasticity, headache, dysarthria, psychosis, mood disturbances, cognitive decline, and dementia (Manyam., 2005. PubMed ID: 15734663; Nicolas et al., 2013. PubMed ID: 24065723). Abnormal deposit of calcium in the brain is a common finding usually associated with aging. However, IBGC is rare, with less than 1/1,000,000 people affected worldwide (Ellie et al., 1989. PMID: 2927646). See also Sobrido et al., 2014. PMID: 20301594.

Genetics

IBGC is genetically heterogeneous. Although most cases are familial with autosomal dominant inheritance, simplex cases with no apparent family history have been also reported. To date, four genes have been implicated in the disease: SLC20A2, PDGFB, PDGFRB and XPR1 (Wang et al., 2012. PubMed ID: 22327515; Keller et al., 2013. PubMed ID: 23913003; Nicolas et al., 2013. PubMed ID: 23255827; Legati et al., 2015. PubMed ID: 25938945).

About 85 pathogenic variants have been reported both in familial and apparently simplex cases from various ethnic and geographic populations (Human Gene Mutation Database).

About half of the variants in the SLC20A2 and PDGFB genes are missense. The other half consists of truncating variants and includes nonsense, splicing and small frameshift insertions and deletions (HGMD). Only one small deletion that is predicted to result in the in-frame deletion of one single amino acid has been reported in the SLC20A2 gene (Wang et al., 2012. PubMed ID: 22327515).

Pathogenic variants in the PDGFRB and XPR1 genes are all of the missense type (HGMD).

PDGFB encodes the platelet-derived growth factor beta (Keller et al., 2013. PubMed ID: 23913003). PDGFRB encodes its main receptor (Nicolas et al., 2013. PubMed ID: 24065723). It has been suggested that the PDGFRB/ PDGFB system is involved in the calcification of vascular smooth muscle cells (Diliberto et al., 1991. PubMed ID: 1905727).

SLC20A2 and XPR1 encode inorganic phosphate transporters (Wang et al., 2012. PubMed ID: 22327515; Legati et al., 2015. PubMed ID: 25938945).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in SLC20A2 account for about 41% of patients with idiopathic basal ganglia calcification (IBGC) (Hsu et al., 2013. PubMed ID: 23334463).

Pathogenic variants in PDGFB account for about 11% of patients with IBGC (Keller et al., 2013. PubMed ID: 23913003).

Pathogenic variants in PDGFRB account for about 10% of patients with IBGC (Nicolas et al., 2013. PubMed ID: 23255827).

Pathogenic variants in XPR1 account for about 4% of patients with IBGC (Legati et al., 2015. PubMed ID: 25938945).

Pathogenic large deletions in the SLC20A2 gene have been reported in about 16% of patients with IBGC who were previously found to be negative for pathogenic sequence variants in the SLC20A2, PDGFB, PDGFRB and XPR1 (David et al., 2016. 27245298).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes 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 coverage as ≥20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Patients with clinical and radiological findings suggestive of idiopathic basal ganglia calcification, including familial and sporadic cases, are candidates for this panel.

Genes

Official Gene Symbol OMIM ID
PDGFB 190040
PDGFRB 173410
SLC20A2 158378
XPR1 605237
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
PGxome®

Citations

  • David et al., 2016. PubMed ID: 27245298
  • Diliberto et al., 1991. PubMed ID: 1905727
  • Ellie et al., 1989. PubMed ID: 2927646
  • Hsu et al., 2013. PubMed ID: 23334463
  • Human Gene Mutation Database (Bio-base).
  • Keller et al., 2013. PubMed ID: 23913003
  • Legati et al., 2015. PubMed ID: 25938945
  • Manyam., 2005. PubMed ID: 15734663
  • Nicolas et al., 2013. PubMed ID: 24065723
  • Sobrido et al., 2014 PubMed ID: 20301594
  • Wang et al., 2012. PubMed ID: 22327515

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.

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

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ORDER OPTIONS

View Ordering Instructions

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.

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