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Congenital Disorders of Glycosylation, Type Ie (CDG Ie) via the DPM1 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
8633 DPM1 81479 81479,81479 $990 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8633DPM181479 81479,81479 $990 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Hongjie Chen

Clinical Features and Genetics

Clinical Features

Congenital disorders of glycosylation (CDGs) are a clinically heterogeneous group of inborn errors of metabolism that are characterized by defects in protein or lipid glycosylation, a form of post-translational modification. These disorders can be further differentiated into several categories depending upon what part of the glycosylation pathway has been disrupted: protein N-linked protein glycosylation defects, which are the most common; O-linked protein glycosylation defects; glycolipid and glycosylphosphatidylinositol (GPI) anchor defects; or multi-pathway defects (Brasil et al. 2018. PubMed ID: 29702557; Jaeken. 2017. PubMed ID: 28484880; Scott et al. 2014. PubMed ID: 24831587).

CDG type Ie, an N-linked glycosylation defect, has been described in approximately fifteen individuals to date (Kim et al. 2000. PubMed ID: 10642597; Bursle et al. 2017. PubMed ID: 27481510; Yang et al. 2013. PubMed ID: 23856421; Vuillaumier-Barrot et al. 2005. PubMed ID: 15771971; Garcia-Silva et al. 2004. PubMed ID: 15669674; Dancourt et al. 2006. PubMed ID: 16641202; Imbach et al. 2000. PubMed ID: 10642602; Medrano et al. 2019. PubMed ID: 30653653; Perez-Cerda et al. 2017. PubMed ID: 28139241). Patients typically presented during the neonatal or infantile stages with hypotonia, retinopathy, progressive microcephaly, seizures, and developmental delays. Other common symptoms included facial dysmorphism and abnormal findings upon neuroimaging, such as delayed myelination and/or cerebellar atrophy. Biochemically, many patients were reported to have elevated creatine kinase and antithrombin III deficiency. Less commonly-reported symptoms included knee contractures, strabismus, nystagmus, and/or hepatosplenomegaly. Clinically less severely-affected patients have also been reported. Two siblings with enzymatic, cellular, and molecular-confirmed CDG Ie were found to have ataxia as the dominant phenotype (Dancourt et al. 2006. PubMed ID: 16641202).

Genetics

Congenital disorder of glycosylation (CDG) type Ie is inherited in an autosomal recessive manner. The DPM1 gene encodes a mannosyltransferase that catalyzes the transfer of the sixth mannose to a lipid-linked oligosaccharide precursor (Gandini et al. 2017. PubMed ID: 28743912). Several missense pathogenic variants, one splice site pathogenic variant, two small frameshift deletions, and one large deletion have been reported in this gene to date (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Due to the low incidence of this disorder, clinical sensitivity cannot be estimated at this time. Only one large deletion has been reported in this gene (Human Gene Mutation Database). Analytical sensitivity should be high as the great majority of reported variants are detectable by sequencing.

Testing Strategy

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV-calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This test provides full coverage of all coding exons of the DPM1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions where pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing.

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 test include individuals with clinical symptoms consistent with CDG Ie, patients with demonstrated dolichol-phosphate-mannose synthase deficiency, and/or patients with accumulation of Man5GlcNAc2 lipid-linked oligosaccharide. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in DPM1.

Gene

Official Gene Symbol OMIM ID
DPM1 603503
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Congenital Disorder Of Glycosylation Type 1E AR 608799

Citations

  • Brasil et al. 2018. PubMed ID: 29702557
  • Bursle et al. 2017. PubMed ID: 27481510
  • Dancourt et al. 2006. PubMed ID: 16641202
  • Gandini et al. 2017. PubMed ID: 28743912
  • Garcia-Silva et al. 2004. PubMed ID: 15669674
  • Imbach et al. 2000. PubMed ID: 10642602
  • Jaeken. 2017. PubMed ID: 28484880
  • Kim et al. 2000. PubMed ID: 10642597
  • Medrano et al. 2019. PubMed ID: 30653653
  • Perez-Cerda et al. 2017. PubMed ID: 28139241
  • Scott et al. 2014. PubMed ID: 24831587
  • Vuillaumier-Barrot et al. 2005. PubMed ID: 15771971
  • Yang et al. 2013. PubMed ID: 23856421

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

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View Ordering Instructions

1) Select Test Method (Platform)


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.
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