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Phosphoglycerate Dehydrogenase Deficiency and Neu-Laxova Syndrome 1 via the PHGDH Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
7911 PHGDH 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7911PHGDH81479 81479,81479 $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

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

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

Phosphoglycerate dehydrogenase deficiency is a rare inborn error of the amino acid L-serine biosynthesis that is characterized by congenital microcephaly, severe psychomotor retardation, hypertonia, intractable seizures, and growth retardation. Enzyme assays show significant decreased activity of 3’-phosphoglycerate dehydrogenase in patient fibroblasts (Klomp et al 2000). The major biochemical abnormalities associated with this disease are low concentrations of L-serine, D-serine, and glycine in cerebrospinal fluid. This deficiency is severe, but potentially treatable (Jaeken et al 1996).

Neu-Laxova syndrome 1 is a rare inborn disorder characterized by a recognizable pattern of malformations leading to prenatal or early postnatal lethality. The main features of the disease include significant fetal growth restriction, microcephaly, distinct facial appearance, ichthyosis and skeletal anomalies. Neu-Laxova syndrome 1 represents the severe end of serine-deficiency disorders (Shaheen et al 2014; Acuna-Hidalgo et al. 2014).

Genetics

Phosphoglycerate dehydrogenase deficiency is inherited in an autosomal recessive manner and caused by pathogenic variants in the PHGDH gene encoding this enzyme. Pathogenic variants reported in the PHGDH gene include missense, nonsense and one small deletion (Klomp et al 2000; Tabatabaie et al 2009). Missense pathogenic variants either primarily affect substrate or cofactor binding and result in very low residual enzymatic activity. Some even lead to almost undetectable enzyme activities (Tabatabaie et al 2009). Large deletions and duplications have not been discovered yet. Disease severity correlates with the degree of PHGDH inactivation.

Neu-Laxova syndrome 1 is inherited in an autosomal recessive manner. Neu-Laxova syndrome 1 and phosphoglycerate dehydrogenase deficiency are allelic disorders. The reported cases of Neu-Laxova syndrome 1 are caused by homozygous missense variants in PHGDH gene (Shaheen et al 2014; Acuna-Hidalgo et al. 2014).

Clinical Sensitivity - Sequencing with CNV PG-Select

For the PHGDH gene, clinical sensitivity in large cohort of patients with phosphoglycerate dehydrogenase deficiency or Neu-Laxova syndrome 1 is unavailable in the literature due to reports only of individual cases. No large deletions and duplications have been reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the PHGDH gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

PHGDH sequencing test is recommended for patients suspected to have phosphoglycerate dehydrogenase deficiency or Neu-Laxova syndrome 1. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PHGDH.

Gene

Official Gene Symbol OMIM ID
PHGDH 606879
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Acuna-Hidalgo R. et al. 2014. American Journal of Human Genetics. 95: 285-93. PubMed ID: 25152457
  • Human Gene Mutation Database (Bio-base).
  • Jaeken J. et al. 1996. Archives of Disease in Childhood. 74: 542-5. PubMed ID: 8758134
  • Klomp L.W. et al. 2000. American Journal of Human Genetics. 67: 1389-99. PubMed ID: 11055895
  • Shaheen R. et al. 2014. American Journal of Human Genetics. 94: 898-904. PubMed ID: 24836451
  • Tabatabaie L. et al. 2009. Human Mutation. 30: 749-56. PubMed ID: 19235232

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

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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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