Congenital Disorders of Glycosylation Panel

  • bpg-method PLUS
  • bpg-method SEQ
  • bpg-method DEL/DUP

Test code: ME1901

The Blueprint Genetics Congenital Disorders of Glycosylation Panel is a 47 gene test for genetic diagnostics of patients with clinical suspicion of disorder of glycoprotein metabolism.

The most types of congenital disorders of N-linked glycolysation are inherited in autosomal recessive manner. MGAT1, ALG13, SLC35A2 and SSR4-related disorders are inherited in X-linked manner. In addition to congenital disorders of N-linked glycolysation, this Panel has differential diagnostics power to rare phenotypes with overlapping symptoms such as GEN-related myopathy and ATP6V0A2- related cutis laxa. This Panel is included in the Comprehensive Metabolism Panel.

About Congenital Disorders of Glycosylation

Congenital disorders of N-linked glycolysation are a genetically and phenotypically very heterogenous group of diseases of N-linked oligosaccharides. The deficiencies are caused by mutations in the genes encoding enzymes in the N-linked synthetic pathway. Defective enzymes cause defects in the glycolysation of tissue proteins or lipids. There are 42 different enzymes in the pathway; any of them may be mutated and cause a disorder belonging to this group. Different mutated enzymes cause different phenotypes. Most commonly, symptoms begin in the early infancy. Manifestations range from mild to severe, involving only protein-losing enteropathy and hypoglycemia or severe developmental delay with malfunction of several organs. Sometimes the disorder may be fatal. Most patients require nutrition supplements. Most of the individual disorders have been observed only in a very limited number of patients. The most common ones are PMM2-related disorder (circa 700 patients reported), MPI-related disorder (>20 patients) and ALG6-related disorder (>30 patients). Other types of disorder are extreme rare.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

Genes in the Congenital Disorders of Glycosylation Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
ALG1* Congenital disorder of glycosylation AR 13 42
ALG2 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 4 4
ALG3 Congenital disorder of glycosylation AR 5 14
ALG6 Congenital disorder of glycosylation AR 6 25
ALG8 Congenital disorder of glycosylation AR 8 15
ALG9 Congenital disorder of glycosylation AR 3 4
ALG11 Congenital disorder of glycosylation AR 8 9
ALG12 Congenital disorder of glycosylation AR 8 13
ALG13 Congenital disorder of glycosylation XL 3 6
ATP6V0A2 Cutis laxa, Wrinkly skin syndrome AR 16 52
B3GLCT Peters-plus syndrome AR 8
B4GALT1 Congenital disorder of glycosylation AR 1 2
COG1 Congenital disorder of glycosylation AR 2 2
COG4 Congenital disorder of glycosylation AR 6 4
COG5 Congenital disorder of glycosylation AR 1 9
COG6 Congenital disorder of glycosylation AR 4 7
COG7 Congenital disorder of glycosylation AR 3 4
COG8 Congenital disorder of glycosylation AR 3 5
DDOST Congenital disorder of glycosylation AR 2 2
DHDDS Retinitis pigmentosa AR 1 3
DOLK Congenital disorder of glycosylation AR 7 7
DPAGT1 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 12 28
DPM1 Congenital disorder of glycosylation AR 7 9
DPM2 Congenital disorder of glycosylation AR 2 2
DPM3 Congenital disorder of glycosylation AR 1 1
GMPPA Alacrima, achalasia, and mental retardation syndrome AR 5 9
GNE Inclusion body myopathy, Nonaka myopathy, Sialuria AD/AR 32 193
MAGT1 Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia XL 4 10
MAN1B1 Mental retardation AR 5 21
MGAT2 Congenital disorder of glycosylation AR 5 5
MOGS Congenital disorder of glycosylation AR 5 5
MPDU1 Congenital disorder of glycosylation AR 4 5
MPI Congenital disorder of glycosylation AR 8 19
PGM1 Congenital disorder of glycosylation AR 9 24
PMM2 Congenital disorder of glycosylation AR 37 119
RFT1 Congenital disorder of glycosylation AR 7 7
RPN2 Congenital disorder of glycosylation AD/AR 1
SEC23B Anemia, dyserythropoietic congenital AR 12 88
SLC35A1 Congenital disorder of glycosylation AR 1 2
SLC35A2 Congenital disorder of glycosylation XL 7 13
SLC35C1 Congenital disorder of glycosylation, Leukocyte adhesion deficiency AR 4 7
SRD5A3* Kahrizi syndrome, Congenital disorder of glycosylation AR 9 13
SSR4 Congenital disorder of glycosylation XL 2 6
STT3A Congenital disorder of glycosylation AR 1 1
STT3B Congenital disorder of glycosylation AR 1 2
TMEM165 Congenital disorder of glycosylation AR 4 6
TUSC3 Mental retardation AR 3 13

*Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Gene Genomic location HG19 HGVS RefSeq RS-number Comment Reference
COG6 Chr13:40273614 c.1167-24A>G NM_020751.2 rs730882236
STT3B Chr3:31663820 c.1539+20G>T NM_178862.1
TMEM165 Chr4:56284334 c.792+182G>A NM_018475.4 rs793888506

The strengths of this test include:

  • Blueprint Genetics is one of the few laboratories worldwide with CAP and ISO-15189 accreditation for NGS panels and CLIA certification
  • Superior sequencing quality
  • Careful selection of genes based on current literature, our experience and the most current mutation databases
  • Transparent and easy access to quality and performance data at the patient level that are accessible via our Nucleus portal
  • Transparent and reproducible analytical validation for each panel (see Test performance section; for complete details, see our Analytic Validation)
  • Sequencing and high resolution del/dup analysis available in one test
  • Inclusion of non-coding disease causing variants where clinically indicated (please see individual Panel descriptions)
  • Interpretation of variants following ACMG variant classification guidelines
  • Comprehensive clinical statement co-written by a PhD geneticist and a clinician specialist

 

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Variants in regulatory or non-coding regions of the gene unless otherwise indicated (please see Non-coding disease causing variants covered by the panel). This mean for instance intronic variants locating deeper than 15 nucleotides from the exon-intron boundary.

 

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Disorders caused by long repetitive sequences (e.g. trinucleotide repeat expansions)

 

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Blueprint Genetics offers a comprehensive Congenital Disorders of Glycosylation Panel that covers classical genes associated with ATP6V0A2-related cutis laxa, disorder of glycoprotein metabolism and GEN-related myopathy. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

Find more info in Support

Choose an analysis method

$ $ 1700
$ $ 1000
$ $ 1900
Total $
Order now

ICD & CPT codes

CPT codes

SEQ 81479
DEL/DUP 81479


ICD codes

Commonly used ICD-10 codes when ordering the Congenital Disorders of Glycosylation Panel

ICD-10 Disease
E77.9 Disorder of glycoprotein metabolism

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Subscribe to our newsletter