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Isolated Foveal Hypoplasia Type 2 (FVH2) via the SLC38A8 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
8299 SLC38A8 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8299SLC38A881479 81479,81479 $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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

  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

Foveal hypoplasia (FVH) is a congenital disorder, which is often associated with other anatomical ocular disorders, such as aniridia, microphthalmia, achromatopsia and albinism. Isolated Foveal hypoplasia (IFVH) rarely has been reported (Oliver et al. 1987; Curran and Robb 1976). FVH is clinically characterized by absent or abnormal foveal depression, incursion of inner retinal layers in the presumed foveal area, short photoreceptor outer segments and optic nerve decussation defects. Other symptoms include decreased visual acuity and nystagmus (Oliver et al. 1987; Curran and Robb 1976; Mota et al. 2012; Al-Araimi et al. 2013; Thomas et al. 2014; Perez et al. 2014).

Genetics

Pathogenic variants in SLC38A8 have been reported to be causative for autosomal recessive foveal hypoplasia type 2 (FVH2). SLC38A8 belongs to the SLC38 gene family, which is involved in transfer of glutamine from astrocytes to neurons in the central nervous system, ammonia detoxification and gluconeogenesis in the liver, and the renal response to acidosis (Mackenzie and Erickson 2004).

SLC38A8 encodes a putative sodium-dependent amino-acid/proton antiporter, which is shown to be solely expressed in the eye (Perez et al. 2014). So far, about 10 pathogenic variants (missense/nonsense, small and gross deletions) in SLC38A8 have been reported that are causative for FVH2 (Human Gene Mutation Database; Poulter et al. 2013; Perez et al. 2014). In addition, common variants in SLC38A8 have been shown to modestly affect foveal thickness in the general population (Poulter et al. 2013).

Autosomal dominant foveal hypoplasia type 1 (FVH1) has also been reported in a few families, due to heterozygous pathogenic variants in PAX6, which is the major causative gene for Aniridia (Azuma et al. 1996; Hingorani et al. 2009; Thomas et al. 2014).

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity cannot be precisely estimated due to heterogeneity and a limited number of documented cases of isolated FVH (IFVH). The majority of the reported SLC38A8 mutations are detectable by sequencing. One gross deletion has been reported in this gene (Poulter et al. 2013; Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the SLC38A8 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

All patients with symptoms suggestive of foveal hypoplasia described in the clinical feature section are candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SLC38A8.

Gene

Official Gene Symbol OMIM ID
SLC38A8 615585
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Al-Araimi M, Pal B, Poulter JA, Genderen MM van, Carr I, Cudrnak T, Brown L, Sheridan E, Mohamed MD, Bradbury J, Ali M, Inglehearn CF, Toomes C. 2013. A new recessively inherited disorder composed of foveal hypoplasia, optic nerve decussation defects and anterior segment dysgenesis maps to chromosome 16q23. 3-24.1. Molecular vision 19: 2165. PubMed ID: 24194637
  • Azuma N, Nishina S, Yanagisawa H, Okuyama T, Yamada M. 1996. PAX6 missense mutation in isolated foveal hypoplasia. Nat. Genet. 13: 141–142. PubMed ID: 8640214
  • Curran RE, Robb RM. 1976. Isolated foveal hypoplasia. Arch. Ophthalmol. 94: 48–50. PubMed ID: 1247409
  • Hingorani M, Williamson KA, Moore AT, Heyningen V van. 2009. Detailed ophthalmologic evaluation of 43 individuals with PAX6 mutations. Investigative ophthalmology & visual science 50: 2581–2590. PubMed ID: 19218613
  • Human Gene Mutation Database (Bio-base).
  • Mackenzie B, Erickson JD. 2004. Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family. Pflugers Arch. 447: 784–795. PubMed ID: 12845534
  • Mota Á, Fonseca S, Carneiro Â, Magalhães A, Brandão E, Falcão-Reis F. 2012. Isolated Foveal Hypoplasia: Tomographic, Angiographic and Autofluorescence Patterns. Case Rep Ophthalmol Med 2012: PubMed ID: 22900218
  • Oliver MD, Dotan SA, Chemke J, Abraham FA. 1987. Isolated foveal hypoplasia. British journal of ophthalmology 71: 926–930. PubMed ID: 3427001
  • Perez Y, Gradstein L, Flusser H, Markus B, Cohen I, Langer Y, Marcus M, Lifshitz T, Kadir R, Birk OS. 2014. Isolated foveal hypoplasia with secondary nystagmus and low vision is associated with a homozygous SLC38A8 mutation. European Journal of Human Genetics 22: 703–706. PubMed ID: 24045842
  • Poulter JA, Al-Araimi M, Conte I, Genderen MM van, Sheridan E, Carr IM, Parry DA, Shires M, Carrella S, Bradbury J, Khan K, Lakeman P, Sergouniotis PI, Webster AR, Moore AT, Pal B, Mohamed MD, Venkataramana A, Ramprasad V, Shetty R, Saktivel M, Kumaramanickavel G, Tan A, Mackey DA, Hewitt AW, Banfi S, Ali M, Inglehearn CF, Toomes C. 2013. Recessive Mutations in SLC38A8 Cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism. The American Journal of Human Genetics 93: 1143–1150. PubMed ID: 24290379
  • Thomas S, Thomas MG, Andrews C, Chan W-M, Proudlock FA, McLean RJ, Pradeep A, Engle EC, Gottlob I. 2014. Autosomal-dominant nystagmus, foveal hypoplasia and presenile cataract associated with a novel PAX6 mutation. Eur. J. Hum. Genet. 22: 344–349. PubMed ID: 23942204

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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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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.
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