DNA icon

Achromatopsia (ACHM) via the GNAT2 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
GNAT2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9985GNAT281479 81479,81479 $990 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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 platform).

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

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

For Sanger Sequencing click here.

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


  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

Achromatopsia (ACHM) is a congenital, autosomal recessive retinal disorder, which is characterized by total color blindness, decreased visual acuity (<0.2), photophobia (lower than 20/200), nystagmus and absence of cone-mediated electroretinographic amplitudes (Kohl et al. 2005; Pang et al. 2010). Estimated prevalence is 1/30,000 (Kohl et al. 2002).


ACHM is a heterogeneous disorder. Pathogenic variants in CNGA3, CNGB3, GNAT2, PDE6C and PDE6H have been reported to be causative for autosomal recessive ACHM (Ouechtati et al. 2011; Greenberg et al. 2014). CNGA3 and CNGB3 are the major causative genes for ACHM (Kohl et al. 2005).

The GNAT2 gene encodes the alpha subunit of cone transducin, the G  protein that couples the cone pigments to cGMP-phosphodiesterase in phototransduction pathway of the visual cycle. Also, GNAT2 pathogenic variants may  be implicated in other forms of retinal dystrophy with cone dysfunction. So far, about 10 causative variants have been identified (missense/nonsense, splicing, small deletions and insertions and large deletion) (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Approximately ~2% of achromatopsia cases are due to pathogenic variants in GNAT2 (Kohl et al. 2002).

So far, only a single exon-level deletion has been reported (Kohl et al. 2002).

Testing Strategy

This test provides full coverage of all coding exons of the GNAT2 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 GNAT2.


Official Gene Symbol OMIM ID
GNAT2 139340
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Achromatopsia 4 613856


  • Greenberg J.P. et al. 2014. Jama Ophthalmology. 132: 437-45. PubMed ID: 24504161
  • Human Gene Mutation Database (Bio-base).
  • Kohl S. et al. 2002. American Journal of Human Genetics. 71: 422-5. PubMed ID: 12077706
  • Kohl S. et al. 2002. American Journal of Human Genetics. 71: 422-5. PubMed ID: 12077706
  • Kohl S. et al. 2002. American Journal of Human Genetics. 71: 422-5. PubMed ID: 12077706
  • Kohl S. et al. 2002. American Journal of Human Genetics. 71: 422-5. PubMed ID: 12077706
  • Kohl S. et al. 2005. European Journal of Human Genetics: Ejhg. 13: 302-8. PubMed ID: 15657609
  • Kohl S. et al. 2005. European Journal of Human Genetics: Ejhg. 13: 302-8. PubMed ID: 15657609
  • Ouechtati F. et al. 2011. Journal of Human Genetics. 56: 22-8. PubMed ID: 21107338
  • Pang J.J. et al. 2010. Advances in Experimental Medicine and Biology. 664: 639-46. PubMed ID: 20238068


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

loading Loading... ×


An error has occurred while calculating the price. Please try again or contact us for assistance.

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.
Total Price: loading
Patient Prompt Pay Price: loading
A patient prompt pay discount is available if payment is made by the patient and received prior to the time of reporting.
Show Patient Prompt Pay Price
Copy Text to Clipboard