Hyperammonemia and Urea Cycle Disorder Panel

Updated
Summary
  • Is a 49 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with hyperammonemia or a clinical suspicion of a disorder of urea cycle metabolism. The genes on this panel are included in the Comprehensive Metabolism Panel.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

49

Test code

ME1601

Panel size

Large

CPT codes
81479

Summary

The Blueprint Genetics Hyperammonemia and Urea Cycle Disorder Panel (test code ME1601):

ICD codes

Commonly used ICD-10 code(s) when ordering the Hyperammonemia and Urea Cycle Disorder Panel

ICD-10 Disease
E72.20 Disorder of urea cycle metabolism
E72.4 Ornithine transcarbamylase deficiency
E72.4 Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome
E71.30 Fatty acid oxidation disorder
E71.121 Organic acidemias
E72.20 Citrin deficiency

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

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. Read more about our sample requirements here.

Congenital urea cycle disorders are the result of defects in the metabolism of nitrogen waste. Deficiency of any of the enzymes in the urea cycle results in an excess of ammonia or other precursor metabolites in the blood. Normally, urea production lowers the ammonia levels in the blood but in the case of defective enzymes, the urea cycle is disturbed. Infants with urea cycle disorders (UCDs) develop cerebral edema, lethargy, hypothermia, neurologic signs and coma, often shortly after birth. Partial, or milder, UCDs are possible if the affected enzyme is positioned in a later phase of the urea cycle. Patients with UCDs may present with hyperammonemia often triggered by stress or illness. The most common primary hyperammonemia is X-linked recessive ornithine transcarbamylase deficiency caused by mutations in the OTC gene. The estimated prevalence is 1:56,000. Prevalence estimates for the other specific urea cycle disorders are 1:200,000 for ASL- and ASS1-related deficiencies and <1:1,000,000 for ARG1, CPS1 and NAGS-related deficiencies. The diagnostic yield ranges from 50% to 80% for different primary urea cycle disorders. In addition to congenital UCDs, this panel has the ability to diagnose other diseases of early phase hyperammonemia and other inborn errors of metabolism showing similar and overlapping symptoms. These include organic acidemias and fatty acid oxidation disorders. In addition, rare syndromes, such as hyperornithinemia-hyperammonemia-homocitrullinuria syndrome and citrin deficiency with hyperammonia symptoms are diagnosed with this panel.

Genes in the Hyperammonemia and Urea Cycle Disorder Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ACADM Acyl-CoA dehydrogenase, medium chain, deficiency AR 104 169
ACADS Acyl-CoA dehydrogenase, short-chain, deficiency AR 43 81
ACADVL Acyl-CoA dehydrogenase, very long chain, deficiency AR 119 282
ARG1 Hyperargininemia AR 28 54
ASL Argininosuccinic aciduria AR 56 162
ASS1 Citrullinemia AR 70 153
BCKDHA Maple syrup urine disease AR 57 98
BCKDHB Maple syrup urine disease AR 87 103
CA5A* Carbonic anhydrase VA deficiency AR 6 7
CPS1 Carbamoylphosphate synthetase I deficiency AR 61 269
CPT1A Carnitine palmitoyltransferase deficiency AR 60 51
CPT2 Carnitine palmitoyltransferase II deficiency AR 72 111
DBT Maple syrup urine disease AR 39 75
DLD Dihydrolipoyl dehydrogenase deficiency AR 36 21
ETFA Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 8 29
ETFB Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 6 15
ETFDH Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 43 190
GLUD1* Hyperammonemia-hyperinsulinism, Hyperinsulinemic hypoglycemia AD/AR 14 38
GLUL Glutamine deficiency, congenital AR 4 3
HADHA Trifunctional protein deficiency, Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency AR 65 71
HADHB Trifunctional protein deficiency AR 20 65
HCFC1 Combined methylmalonic acidemia and hyperhomocysteinemia XL 9 17
HLCS Holocarboxylase synthetase deficiency AR 34 47
HMGCL 3-hydroxy-3-methylglutaryl-CoA lyase deficiency AR 24 60
HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 deficiency AR 9 30
IVD Isovaleric acidemia AR 51 90
MCCC1 3-Methylcrotonyl-CoA carboxylase 1 deficiency AR 40 105
MCCC2 3-Methylcrotonyl-CoA carboxylase 2 deficiency AR 24 114
MMAA Methylmalonic acidemia AR 61 75
MMAB Methylmalonic acidemia AR 31 40
MMACHC Methylmalonic aciduria and homocystinuria AR 59 93
MMADHC Methylmalonic aciduria and homocystinuria AR 16 13
MUT Methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency AR 159 366
NAGS N-acetylglutamate synthase deficiency AR 12 48
NBAS Infantile liver failure syndrome 2, Short stature, optic nerve atrophy, and Pelger-Huet anomaly (SOPH syndrome) AR 23 43
OAT Gyrate atrophy of choroid and retina AR 67 71
OTC Ornithine transcarbamylase deficiency XL 343 513
PC Pyruvate carboxylase deficiency AR 32 41
PCCA Propionic acidemia AR 66 125
PCCB# Propionic acidemia AR 68 115
SLC22A5 Carnitine deficiency, systemic primary AR 98 151
SLC25A13 Citrin deficiency AR 24 113
SLC25A15* Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome AR 24 36
SLC25A20 Carnitine-acylcarnitine translocase deficiency AR 15 42
SLC7A7 Lysinuric protein intolerance AR 55 67
SUCLA2 Mitochondrial DNA depletion syndrome AR 9 29
SUCLG1 Mitochondrial DNA depletion syndrome AR 12 28
TMEM70 Mitochondrial complex V (ATP synthase) deficiency AR 12 18
UMPS Orotic aciduria AR 3 12

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by Hyperammonemia and Urea Cycle Disorder Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ACADM Chr1:76200457 c.388-19T>A NM_000016.4
ACADM Chr1:76211473 c.600-18G>A NM_000016.4 rs370523609
ACADVL Chr17:7123160 c.-144_-132delCCCAGCATGCCCCinsT NM_000018.3
ACADVL Chr17:7125469 c.822-27C>T NM_001270447.1 rs374911841
ACADVL Chr17:7125485 c.822-11T>G NM_001270447.1
ACADVL Chr17:7126199 c.1146+15C>T NM_001270447.1 rs202237278
ACADVL Chr17:7126948 c.1252-15A>G NM_001270447.1 rs765390290
ACADVL Chr17:7127894 c.1747+23C>T NM_001270447.1
ARG1 Chr6:131901748 c.306-611T>C NM_000045.3
ASS1 Chr9:133327601 c.-5-10C>G NM_000050.4 rs375136377
ASS1 Chr9:133332669 c.175-1119G>A NM_000050.4
ASS1 Chr9:133355236 c.773+49C>T NM_000050.4 rs763389916
BCKDHA Chr19:41930736 c.*223T>A NM_000709.3 rs373164531
CPS1 Chr2:211539387 c.4102-239A>G NM_001875.4
DBT Chr1:100672742 c.1018-550A>G NM_001918.3 rs796052135
ETFDH Chr4:159593534 c.-75A>G NM_004453.2
ETFDH Chr4:159602711 c.176-636C>G NM_004453.2
HADHB Chr2:26500642 c.442+614A>G NM_000183.2
HADHB Chr2:26500691 c.442+663A>G NM_000183.2
HCFC1 ChrX:153237261 c.-970T>C NM_005334.2 rs398122908
MCCC2 Chr5:70898313 c.384-20A>G NM_022132.4 rs770917710
MCCC2 Chr5:70939634 c.1073-12C>G NM_022132.4 rs1280511914
MUT Chr6:49427219 c.-39-1G>A NM_000255.3
NAGS Chr17:42078968 c.-3063C>A NM_153006.2
NBAS Chr2:15567431 c.2423+404G>C NM_015909.3
OTC ChrX:38202566 c.-9384G>T NM_000531.5
OTC ChrX:38211584 NM_000531.5 rs191615506
OTC ChrX:38211793 c.-157T>G NM_000531.5
OTC ChrX:38211808 c.-142G>A NM_000531.5
OTC ChrX:38211811 c.-139A>G NM_000531.5
OTC ChrX:38211834 c.-116C>T NM_000531.5
OTC ChrX:38211835 c.-115C>T NM_000531.5
OTC ChrX:38211844 c.-106C>A NM_000531.5 rs749748052
OTC ChrX:38260946 c.540+265G>A NM_000531.5
OTC ChrX:38269404 c.867+1126A>G NM_000531.5
OTC ChrX:38272343 c.1005+1091C>G NM_000531.5
PC Chr11:66620883 c.1369-29A>G NM_000920.3
PCCA Chr13:100958030 c.1285-1416A>G NM_000282.3
PCCB Chr3:136003251 c.714+462A>G NM_001178014.1
SLC22A5 Chr5:131714054 c.394-16T>A NM_003060.3 rs775097754
SLC22A5 Chr5:131722665 c.825-52G>A NM_003060.3

Test Strengths

The strengths of this test include:
  • CAP and ISO-15189 accredited laboratory
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test Limitations

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: PCCB (NM_001178014:4). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
This test may not reliably detect the following:
  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

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.

The Blueprint Genetics hyperammonemia and urea cycle disorder panel covers classical genes associated with disorder of urea cycle metabolism, ornithine transcarbamylase deficiency, Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, fatty acid oxidation disorder, organic acidemias and citrin deficiency. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999
11-50 bps 99.13% (2,524/2,546) >99.9999
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. 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. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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