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Achromatopsia (ACHM) via the ATF6 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
12627 ATF6 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
12627ATF681479 81479,81479 $890 Order Options and Pricing

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).

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

Achromatopsia (ACHM) is a congenital, autosomal recessive retinal disorder characterized by total color blindness, decreased visual acuity (lower than 20/200), photophobia, nystagmus and absence of cone-mediated electroretinographic amplitudes at birth or early infancy (Kohl et al. 2005. PubMed ID: 15657609; Kohl et al. 2015. PubMed ID: 26029869; Pang et al. 2010. PubMed ID: 20238068). Estimated prevalence is 1/30,000 (Kohl et al. 2002. PubMed ID: 12077706).

With the advent of gene therapy and other types of treatments, the identification of causative genes and variants is becoming increasingly important.

Please see the links for clinical trials and management options below:

Management

ACHM Clinical trials

Genetics

ACHM is a heterogeneous disorder. To date, pathogenic variants in CNGA3, CNGB3, GNAT2, PDE6C, ATF6 and PDE6H have been reported to be causative for autosomal recessive ACHM (Ouechtati et al. 2011. PubMed ID: 21107338; Greenberg et al. 2014. PubMed ID: 24504161; Mastey et al. 2019. PubMed ID: 31237654). CNGA3 and CNGB3 are the major causative genes for ACHM (Kohl et al. 2005. PubMed ID: 15657609). A frameshift protein truncating variant in CNGB3 (c.1148del, p.Thr383Ilefs*13) has been reported as a predominant pathogenic variant (Kohl et al. 2005. PubMed ID: 15657609; Nishiguchi et al. 2005. PubMed ID: 15712225; Wiszniewski et al. 2007. PubMed ID: 17265047). This variant has been reported at a frequency of 0.2% in general population (http://gnomad.broadinstitute.org/variant/8-87656008-AG-A). To our knowledge, de novo variants have not been documented causative in the genes associated with ACHM (HGMD-Human Gene Mutation Database).

ATF6 encodes photoreceptor specific- activating transcription factor 6A, which is a key regulator of the unfolded protein response (UPR) and cellular endoplasmic reticulum (ER) homeostasis. These functions are essential for retina and photoreceptor survival (Kohl et al. 2015. PubMed ID: 26029869; Xu et al. 2015. PubMed ID: 26070061). Mice lacking ATF6 have been shown to have normal retinal morphology and function at a young age, but with increasing age they develop dysfunction of photoreceptor cells (Xu et al. 2015. PubMed ID: 26070061).

So far, about 15 causative ATF6 variants have been identified (missense/nonsense, splicing, small deletions and duplications that result in frameshift and protein truncation) (HGMD).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in ATF6 are a rare cause of Achromatopsia. Kohl et al. reported that in their patient cohort, ~1% of European-ancestry individuals with Achromatopsia carried pathogenic variants in ATF6 (Kohl et al. 2015. PubMed ID: 26029869).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the ATF6 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 affected by Achromatopsia are candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ATF6. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known pathogenic variants or to confirm research results.

Gene

Official Gene Symbol OMIM ID
ATF6 605537
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Achromatopsia 7 AR 616517

Citations

  • Greenberg et al. 2014. PubMed ID: 24504161
  • Human Gene Mutation Database (Bio-base).
  • Kohl et al. 2002. PubMed ID: 12077706
  • Kohl et al. 2005. PubMed ID: 15657609
  • Kohl et al. 2015. PubMed ID: 26029869
  • Mastey et al. 2019. PubMed ID: 31237654
  • Nishiguchi et al. 2005. PubMed ID: 15712225
  • Ouechtati et al. 2011. PubMed ID: 21107338
  • Pang et al. 2010. PubMed ID: 20238068
  • Wiszniewski et al. 2007. PubMed ID: 17265047
  • Xu et al. 2015. PubMed ID: 26070061

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.
Total Price: $
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