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Epilepsy, X-linked, with Variable Learning Disabilities and Behavior Disorders via the SYN1 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
SYN1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8287SYN181479 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

Synapsin I-related X-linked epilepsy with variable learning disabilities and behavior disorders is a rare neurological disorder. The phenotype includes various combinations of epilepsy, macrocephaly, learning difficulties, aggressive behavior or autism with low penetrance (Garcia et al 2004; Fassio et al 2011).

Epilepsy is present in virtually all the male patients. Learning and behavioral disturbances are common among male patients, while only a few males have autism spectrum disorders. Female carriers have normal intelligence and have no record of seizures or aggressive behavior (Garcia et al 2004).


Pathogenic variants in the SYN1 gene are causative for synapsin I-related X-linked epilepsy with variable learning disabilities and behavior disorders, which is inherited in an X-linked recessive manner. This gene is also a predisposing gene to autism spectrum disorders. The SYN1 gene encodes synapsin I, a synaptic vesicle associated protein that may play an important role in neurotransmitter release, synaptogenesis, maintenance of mature synapses and plasticity and neuronal development (Garcia et al 2004; Fassio et al 2011; Cesca et al 2010).

Pathogenic variants in SYN1 include nonsense and missense variants only. No large deletions/duplications in the SYN1 locus have been reported (Garcia et al 2004; Fassio et al 2011; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

Synapsin I-related X-linked epilepsy with variable learning disabilities and behavior disorders is a rare disease. However, certain missense pathogenic variants were discovered in 1.0 and 3.5% of French-Canadian patients with epilepsy and autism, respectively (Fassio et al 2011).

No large deletions or duplications involving the SYN1 gene have been reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the SYN1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test include patients with symptoms suggestive of synapsin I related X-liked epilepsy with variable learning disabilities and behavior disorders.


Official Gene Symbol OMIM ID
SYN1 313440
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Cesca F. et al. 2010. Progress in Neurobiology. 91: 313-48. PubMed ID: 20438797
  • Fassio A. et al. 2011. Human Molecular Genetics. 20: 2297-307. PubMed ID: 21441247
  • Garcia C.C. et al. 2004. Journal of Medical Genetics. 41: 183-6. PubMed ID: 14985377
  • Human Gene Mutation Database (Bio-base).


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)

1) Select Test Type

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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