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Achromatopsia (ACHM) via the CNGA3 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
CNGA3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7607CNGA381479 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


  • 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, and account for ~20-30% and 40-50% of the cases, respectively (Kohl et al. 2005; Wissinger et al. 2001).

The CNGA3 gene encodes the alpha subunit of the cyclic nucleotide-gated cation channel, which is essential for cone phototransduction (Sundin et al. 2000). Over 100 different CNGA3 causative variants (Missense/nonsense, small deletions/insertions and gross deletions) have been reported (Human Gene Mutation Database). The majority of the CNGA3 causative variants are missense, which indicates that CNGA3 peptides are evolutionarily highly conserved, and its function has little tolerance for any amino acid substitution (Chen et al. 2015). The CNGA3 variants p.Arg277Cys, p.Arg283Trp, p.Arg436Trp, and p.Phe547Leu account for ~42% of all CNGA3 causative variants (Wissinger B. et al. 2001). In addition to achromatopsia, CNGA3 causative variants were identified in patients with autosomal recessive progressive cone dystrophy and total color-blindness (Thiadens et al. 2010; Wissinger et al. 2001).

Clinical Sensitivity - Sequencing with CNV PG-Select

Approximately 20-30% of achromatopsia cases are due to pathogenic variants in CNGA3 (Wissinger et al. 2001).

Large deletions or duplications have not been reported so far in CNGA3 (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the CNGA3 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Patients with normal rod response and absence of cone response in ERG findings, and negative for CNGB3 causative variants (Kohl et al. 2009). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CNGA3.


Official Gene Symbol OMIM ID
CNGA3 600053
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Achromatopsia 2 AR 216900

Related Test

Leber Congenital Amaurosis Panel


  • Chen X.T. et al. 2015. International Journal of Ophthalmology. 8: 910-5. PubMed ID: 26558200
  • Greenberg J.P. et al. 2014. Jama Ophthalmology. 132: 437-45. PubMed ID: 24504161
  • Human Gene Mutation Database (Bio-base).
  • Kohl et al. 2015. Achromatopsia. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301591
  • 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
  • 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
  • Sundin O.H. et al. 2000. Nature Genetics. 25: 289-93. PubMed ID: 10888875
  • Thiadens A.A. et al. 2010. Ophthalmology. 117: 825-30.e1. PubMed ID: 20079539
  • Wissinger B. et al. 2001. American Journal of Human Genetics. 69: 722-37. PubMed ID: 11536077


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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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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