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GM3 Synthase Deficiency via the ST3GAL5 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
ST3GAL5 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4255ST3GAL581479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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.


Genetic Counselors


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

GM3 synthase deficiency (or Amish Infantile Epilepsy Syndrome or Salt and Pepper Mental Retardation Syndrome) is a rare infantile onset neurocutaneous disorder characterized by refractory epilepsy, severe intellectual disability, dysmorphic facial features and hyper- and hypo-pigmented skin maculae on the trunk, face, and extremities. Other variable features include scoliosis, choreoathetosis, spasticity, blindness, deafness, and abnormal EKG (Fragaki et al. 2013; Boccuto et al. 2014).

The onset of epilepsy is accompanied by profound developmental stagnation and regression. Failure to thrive, trouble feeding, and irritability are noticed in the first 2 weeks to 3 months of life. Seizure onset occurs within the first year with multiple type manifestations including generalized tonic-clonic seizures, brief tonic spasms, episodes of eye deviation or startle from sleep. EEG reveals multifocal epileptiform activity. MRI results are initially normal, but show diffuse atrophy as patients age. Mass spectrometry reveals loss of complex gangliosides (Simpson et al. 2004; Fragaki et al. 2013).


GM3 synthase deficiency is inherited in an autosomal recessive manner and is caused by pathogenic variants in the ST3GAL5 gene which encodes GM3 synthase (sialyltransferase). Missense and nonsense variants in ST3GAL5 have been reported in patients with GM3 synthase deficiency. No large deletions/duplications in the ST3GAL5 locus have been reported. Initially described in an Old Order Amish pedigree, GM3 synthase deficiency has subsequently been reported in African-American and French families (Simpson et al. 2004; Fragaki et al. 2013; Boccuto et al. 2014).

GM3 synthase adds sialic acid to lactosylceramide, finally forming ganglioside GM3. The ganglioside GM3 is a glycosphingolipid mainly expressed in neural tissue. One study demonstrated that mitochondrial dysfunction and apoptosis occurred secondary to GM3 synthase deficiency (Fragaki et al. 2013). The authors suggest that mitochondrial defects might contribute to the ganglioside GM3 synthase deficiency phenotype and could explain the clinical similarities between GM3 synthase deficiency and respiratory chain disorders (Fragaki et al. 2013).

Clinical Sensitivity - Sequencing with CNV PG-Select

Clinical sensitivity of ST3GAL5 in a large cohort of patients with ganglioside GM3 synthase deficiency relevant phenotypes is unavailable in the literature because most of the studies are case reports. Analytical sensitivity should be high because all pathogenic variants reported to date are detectable by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the ST3GAL5 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

ST3GAL5 testing should be considered for patients suspected to have GM3 synthase deficiency. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ST3GAL5.


Official Gene Symbol OMIM ID
ST3GAL5 604402
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Amish Infantile Epilepsy Syndrome AR 609056


  • Boccuto L. et al. 2014. Human Molecular Genetics. 23: 418-33. PubMed ID: 24026681
  • Fragaki K. et al. 2013. European Journal of Human Genetics : Ejhg. 21: 528-34. PubMed ID: 22990144
  • Simpson M.A. et al. 2004. Nature Genetics. 36: 1225-9. PubMed ID: 15502825


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

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

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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