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Autosomal Dominant Cone Dystrophy 3 (COD3) and Cone-Rod Dystrophy 14 (CRD14) via the GUCA1A Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
678 GUCA1A$490.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
A mutation analysis in an American five-generation pedigree with 30 living family members identified heterozygous GUCA1A mutations in all affected family members (11/30; ~36%), which segregated with the disease phenotype and was not found in 200 normal controls (Jiang et al., 2005). Another mutation screening in a three-generation Spanish family with ad retinal dystrophy detected a GUCA1A mutation in all affected individuals (5/9; ~55%), which also co-segregated with the disease phenotype and was not found in 200 ethnically matched control individuals (Kamenarova et al., 2013). In another study with 24 unrelated patients (19 patients had adCOD and five patients had adCRD) GUCA1A mutations were identified in four patients (4/24; ~16%) (Kitiratschky et al., 2009). The GUCA1A gene was analyzed in 216 patients with various hereditary retinal disorders in which cones were dysfunctional and five causative mutations in a total of six patients were identified (6/216; ~3%) (Nishiguchi et al., 2004).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 GUCA1A$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity
So far, no gross deletions or duplications have been reported in GUCA1A (The Human Gene Mutation Database).

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Clinical Features
Hereditary cone dystrophies (COD) are clinically and genetically heterogeneous disorders that result in the dysfunction of the cone photoreceptors. Major clinical features include bilateral visual loss, abnormal color vision, central scotomata, variable degrees of nystagmus and photophobia. CODs manifest as progressive or stationary disorders. The stationary subtype CODs occur within the first months of life with pendular nystagmus and photophobia with normal rod function and are better described as cone dysfunction syndromes, whereas progressive CODs usually occur in childhood or early adulthood and patients often develop rod photoreceptor dysfunction in later life. The stationary subtype CODs are uncommon with an incidence of about 1 in 30,000 (Michaelides et al., 2004; Simunovic and Moore, 1998).

Cone rod dystrophies (CORDs/CRDs) are also rare with a worldwide prevalence of ~1 in 40,000. CORDs are characterized by dysfunction or degeneration of cone photoreceptors with relative preservation of rod function in the initial stages. The most common symptoms are photophobia and epiphora in bright light, decreased visual acuity, and dyschromatopsia. Fundus changes may vary from mild pigment granularity to a distinct atrophic lesion in the central macula. As the disease progresses, degeneration of rod photoreceptors also occurs and leads to progressive night blindness and peripheral visual field loss (Hamel, 2007).

COD and CRD are diagnosed mainly on the basis of photopic and scotopic electroretinogram responses, fundoscopy and optical coherence tomography (Jiang and Baehr, 2010).
Genetics
Both COD and CRD exhibit autosomal dominant (ad), autosomal recessive (ar) or X-linked (XL) inheritance. (RetNet). Thus far, the best characterized genes associated with ad COD and CRD are GUCY2D, encoding photoreceptor guanylate cyclase 1 (retGC-1 or GC1), and GUCA1A, encoding the Ca2+-binding protein (GCAP1), which are expressed in the outer segments of the photoreceptors (Jiang and Baehr, 2010). GC1 and GCAP1 play major roles in visual phototransduction, which is a biochemical process responsible for light conversion into electrical signals in the rod and cone cells. In this process, GC1 helps in restoring photoreceptor sensitivity by synthesizing cyclic guanosine monophosphate (cGMP), which is regulated by guanylate cyclase activator proteins (GCAPs: 1 and 2). GCAPs are sensitive to changes in the cytoplasmic Ca2+ concentrations. It has been reported that GCAP2 is activated at lower Ca2+ concentrations than GCAP1 (Hwang et al., 2003). However, GCAP1 and GCAP2 regulate the Ca2+ signaling of GC1 in different ways. At lower cytoplasmic Ca2+ concentrations, GCAP1 interacts with GC1 and stimulates it, and consequently, the cGMP level is restored (Jiang et al., 2005).  Even in the absence of GCAP2, GCAP1alone can restore rod and cone responses, whereas GCAP2 can only partially compensate (Kitiratschky et al., 2009). Thus, GCAP1 plays a major role in regaining the dark-adapted state after excitation of the photoreceptor (Mendez et al., 2001; Pennesi et al., 2003). Disruption of Ca2+ homeostasis, due either to genetic or environmental factors leads to apoptosis of the photoreceptor cells (Baehr and Palczewski., 2007; Garcia-Hoyos et al., 2011). So far, about ten causative mutations (mostly missense) in GUCA1A have been associated with adCOD and adCRD (The Human Gene Mutation Database).
Testing Strategy
This test involves bidirectional DNA Sanger sequencing of all coding exons of the GUCA1A gene. The full coding region of each exon plus ~20 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with a known mutation or to confirm research results.
Indications for Test
All patients with symptoms suggestive of adCOD and adCRD, especially patients with distinctive electrophysiological findings (please see the clinical features section).

Gene

Official Gene Symbol OMIM ID
GUCA1A 600364
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Cone Dystrophy 3 602093
Cone-rod dystrophy 14 602093

Related Test

Name
Cone-Rod Dystrophy Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Baehr W and Palczewski K. 2007. Guanylate cyclase-activating proteins and retina disease. Subcell Biochem 45:71-91. PubMed ID: 18193635
  • Garcia-Hoyos M, Auz-Alexandre CL, Almoguera B, Cantalapiedra D, Riveiro-Alvarez R, Lopez-Martinez MA, Gimenez A, Blanco-Kelly F, Avila-Fernandez A, Trujillo-Tiebas MJ, Garcia-Sandoval B, Ramos C, Ayuso C. 2011. Mutation analysis at codon 838 of the Guanylate Cyclase 2D gene in Spanish families with autosomal dominant cone, cone-rod, and macular dystrophies. Mol. Vis. 17:1103-1109. PubMed ID: 21552474
  • Hamel CP. 2007. Cone rod dystrophies. Orphanet J Rare Dis 1;2:7. PubMed ID: 17270046
  • Human Gene Mutation Database (Bio-base).
  • Hwang JY, Lange C, Helten A, Höppner-Heitmann D, Duda T, Sharma RK, Koch KW. 2003. Regulatory modes of rod outer segment membrane guanylate cyclase differ in catalytic efficiency and Ca(2+)-sensitivity. Eur. J. Biochem. 270: 3814–3821. PubMed ID: 12950265
  • Jiang L, Baehr W. 2010. GCAP1 Mutations Associated with Autosomal Dominant Cone Dystrophy. In: Anderson RE, Hollyfield JG, and LaVail MM, editors. Retinal Degenerative Diseases, New York, NY: Springer New York, p 273–282. PubMed ID: 20238026
  • Jiang L, Katz BJ, Yang Z, Zhao Y, Faulkner N, Hu J, Baird J, Baehr W, Creel DJ, Zhang K. 2005. Autosomal dominant cone dystrophy caused by a novel mutation in the GCAP1 gene (GUCA1A). Mol. Vis. 11:143-51. PubMed ID: 15735604
  • Kamenarova K, Corton M, García-Sandoval B, Fernández-San Jose P, Panchev V, Ávila-Fernández A, López-Molina MI, Chakarova C, Ayuso C, Bhattacharya SS. 2013. Novel GUCA1A Mutations Suggesting Possible Mechanisms of Pathogenesis in Cone, Cone-Rod, and Macular Dystrophy Patients. BioMed Research International 2013: 1–15. PubMed ID: 24024198
  • Kitiratschky VB, Behnen P, Kellner U, Heckenlively JR, Zrenner E, Jägle H, Kohl S, Wissinger B, Koch K-W. 2009. Mutations in the GUCA1A gene involved in hereditary cone dystrophies impair calcium-mediated regulation of guanylate cyclase. Human mutation 30: E782–E796. PubMed ID: 19459154
  • Mendez A, Burns ME, Sokal I, Dizhoor AM, Baehr W, Palczewski K, Baylor DA, Chen J. 2001. Role of guanylate cyclase-activating proteins (GCAPs) in setting the flash sensitivity of rod photoreceptors. Proceedings of the National Academy of Sciences 98:9948-9953. PubMed ID: 11493703
  • Michaelides M. 2004. The cone dysfunction syndromes. British Journal of Ophthalmology 88: 291–297. PubMed ID: 14736794
  • Nishiguchi KM. 2004. A Novel Mutation (I143NT) in Guanylate Cyclase-Activating Protein 1 (GCAP1) Associated with Autosomal Dominant Cone Degeneration. Investigative Ophthalmology & Visual Science 45: 3863–3870. PubMed ID: 15505030
  • Pennesi ME, Howes KA, Baehr W, Wu SM. 2003. Guanylate cyclase-activating protein (GCAP) 1 rescues cone recovery kinetics in GCAP1/GCAP2 knockout mice. Proceedings of the National Academy of Sciences 100: 6783–6788. PubMed ID: 12732716
  • RetNet
  • Simunovic MP, Moore AT. 1998. The cone dystrophies. Eye (Lond) 12 ( Pt 3b):553-565. PubMed ID: 9775217
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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