Cone-Rod Dystrophy Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1337 ABCA4 81408 Add to Order
ADAM9 81479
AIPL1 81479
C21orf2 81479
C8orf37 81479
CABP4 81479
CACNA1F 81479
CACNA2D4 81479
CDHR1 81479
CERKL 81479
CNGB3 81479
CNNM4 81479
CRX 81404
GUCA1A 81479
GUCY2D 81479
KCNV2 81479
PDE6C 81479
PITPNM3 81479
PROM1 81479
PRPH2 81404
RAX2 81479
RDH5 81479
RIMS1 81479
RPGRIP1 81479
SEMA4A 81479
UNC119 81479
Full Panel Price* $1690.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1337 Genes x (26) $1690.00 81404(x2), 81408, 81479(x23) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

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 28 days.

Clinical Sensitivity

A mutation spectrum analysis by Sanger sequencing of eight adCRD-associated genes identified pathogenic variations in ~50% of all adCD (cone dystrophy) and adCRD cases (Kohl et al. 2012). Causative variations were identified in GUCY2D (23%), PRPH2 (11%), GUCA1A (8%), CRX (4%), and PROM1 (2%) genes. No pathogenic variants were detected in AIPL1, UNC119 and PITPNM3, suggesting they may have a minor role in adCD and adCRD . A study based on literature searches (RetNet) reports that the arCRD-genes ABCA4, RPGRIP1, ADAM9 and CERKL are responsible for nearly 40% of arCRD cases, ABCA4 being the major causative gene (den Hollander et al. 2010). Whole exome sequencing in 47 Chinese Families with CRD, identified 14 potential pathogenic variations in 10 families (21.3%). These causative sequence variations were found in 6 of the 25 CRD-associated genes: CNGB3 (6.4%), PDE6C (4.3%), RPGR (4.3%), ABCA4 (2.0%), RPGRIP1 (2.0%), and CACNA1F (2.0%). The authors report that this is the first systemic exome-sequencing analysis of all 25 CRD-associated genes (Huang et al. 2013). All these genes account for only about half of the ad/ar CRD cases, which indicates that there are still many genes that need to be identified (Hamel 2007).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ABCA4$690.00 81479 Add to Order
ADAM9$690.00 81479
AIPL1$690.00 81479
C21orf2$690.00 81479
C8orf37$690.00 81479
CABP4$690.00 81479
CACNA1F$690.00 81479
CACNA2D4$690.00 81479
CDHR1$690.00 81479
CERKL$690.00 81479
CNGB3$690.00 81479
CNNM4$690.00 81479
CRX$690.00 81479
GUCA1A$690.00 81479
GUCY2D$690.00 81479
KCNV2$690.00 81479
PDE6C$690.00 81479
PITPNM3$690.00 81479
PROM1$690.00 81479
PRPH2$690.00 81479
RAX2$690.00 81479
RDH5$690.00 81479
RIMS1$690.00 81479
RPGRIP1$690.00 81479
SEMA4A$690.00 81479
UNC119$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (26) $1290.00 81479(x26) Add to Order
Pricing Comment

# of Genes Ordered

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Over 100

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Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Gross deletions/duplications that are not detectable via Sanger sequencing have been reported in PRPH2, CRX, CNGB3, ABCA4, GUCY2D, CACNA2D4, CNNM4, KCNV2 and CACNA1F (Human Gene Mutation Database).

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Clinical Features

Cone-rod dystrophy (CORD/CRD) is a rare hereditary retinal disorder with a worldwide prevalence of ~1 in 40,000. CRD is 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).


Non syndromic CRD is genetically heterogeneous and exhibits autosomal dominant (AD), autosomal recessive (AR) and, rarely, X-linked (XL) inheritance (Hamel 2007). So far about 25 genes have been implicated in different forms of CRD (RetNet). Causative mutations in the genes ABCA4, ADAM9, CACNA2D4, CDHR1, CERKL, CNGB3, CNNM4, PDE6C, RPGRIP1, C8orf37, C21orf2, KCNV2, CABP4 and RDH5 are inherited in an AR manner. Causative mutations in the genes AIPL1, CRX, GUCA1A, GUCY2D, PITPNM3, PROM1, PRPH2, RAX2, RIMS1, SEMA4A, UNC119 show AD inheritance. CACNA1F and RPGR are the only genes associated with XL-CRD in male patients. Females are often asymptomatic, possibly due to random X inactivation. RPGR is a major gene responsible for ~70% of the XL- Retinitis pigmentosa (RP) cases. Currently, its contribution to the XL-CRD is unknown (Hamel 2007). Testing of the RPGR gene is not included in this NGS panel. However, we do offer Sanger sequencing of RPGR gene, which includes open reading frame 15 (ORF15) sequence analysis. Due to the genetic heterogeneity, screening of all the CRD-associated genes is recommended. Most of the CRD-associated genes are also involved in other types of retinal dystrophies such as RP, macular dystrophies and cone dystrophies. Many of these genes encode proteins that have major roles in disc morphogenesis and the membrane- trafficking of photoreceptors (Sung and Chuang 2010). See individual gene test descriptions for information on molecular biology of gene products.

Testing Strategy

For this CRD NGS panel, we sequence all coding exons of the indicated genes, plus ~20 nucleotides of flanking non-coding intronic DNA. Sequencing is accomplished by capturing relevant regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic and undocumented variants are confirmed by Sanger sequencing.

Indications for Test

All patients with symptoms suggestive of Cone-rod dystrophy (described in the clinical features section) are candidates.


Name Inheritance OMIM ID
Choroidal Dystrophy, Central Areolar 2 613105
Cone Dystrophy 3 602093
Cone Dystrophy 4 613093
Cone-Rod Dystrophy 10 610283
Cone-Rod Dystrophy 11 610381
Cone-Rod Dystrophy 12 612657
Cone-Rod Dystrophy 13 608194
Cone-rod dystrophy 14 602093
Cone-Rod Dystrophy 15 613660
Cone-rod dystrophy 16 614500
Cone-Rod Dystrophy 2 120970
Cone-Rod Dystrophy 3 604116
Cone-Rod Dystrophy 5 600977
Cone-Rod Dystrophy 6 601777
Cone-Rod Dystrophy 7 603649
Cone-Rod Dystrophy 9 612775
Cone-Rod Dystrophy X-Linked 3 300476
Immunodeficiency 13 615518
Jalili Syndrome 217080
Leber Congenital Amaurosis 4 604393
Macular Dystrophy, Vitelliform, Adult-Onset 608161
Night Blindness, Congenital Stationary, Type 2B 610427
Patterned Dystrophy Of Retinal Pigment Epithelium 169150
Retinal Cone Dystrophy 3B 610356
Retinal Cone Dystrophy 4 610478
Retinitis Pigmentosa 26 608380
Stargardt Disease 1 248200

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Achromatopsia via the CNGB3 Gene
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Amelogenesis Imperfecta Sequencing Panel with CNV Detection
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Autosomal Dominant Cone Dystrophy 3 (COD3) and Cone-Rod Dystrophy 14 (CRD14) via the GUCA1A Gene
Autosomal Dominant Cone-Rod Dystrophy via the RIMS1 Gene
Autosomal Dominant Retinitis Pigmentosa Sequencing Panel with CNV Detection
Autosomal Recessive Retinitis Pigmentosa 26 (RP26) via the CERKL Gene
Autosomal Recessive Retinitis Pigmentosa Sequencing Panel with CNV Detection
Comprehensive Inherited Retinal Dystrophies (includes RPGR ORF15) Sequencing Panel with CNV Detection
Cone-Rod Dystrophy (CORDX3) via the CACNA1F Gene
Cone-Rod Dystrophy (CRD11) via the Rax2 (Qrx) Gene
Cone-Rod Dystrophy and Retinitis Pigmentosa via the C8orf37 Gene
Cone-Rod Dystrophy via the ADAM9 Gene
Cone-Rod Dystrophy via the CABP4 Gene
Cone-Rod Dystrophy via the CACNA2D4 Gene
Cone-Rod Dystrophy via the CDHR1 Gene
Cone-Rod Dystrophy via the CNNM4 Gene
Cone-Rod Dystrophy via the KCNV2 Gene
Cone-Rod Dystrophy via the PITPNM3 Gene
Cone-Rod Dystrophy via the UNC119 Gene
Congenital Stationary Night Blindness Sequencing Panel with CNV Detection
Flecked Retina Disorder Sequencing Panel with CNV Detection
Fundus Albipunctatus With or Without Cone Dystrophy via the RDH5 Gene
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Leber Congenital Amaurosis 4 (LCA4) via the AIPL1 Gene
Leber Congenital Amaurosis Sequencing Panel with CNV Detection
Leber Congenital Amaurosis via the CRX Gene
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Stargardt Disease (STGD) and Macular Dystrophies (includes RPGR ORF15) Sequencing Panel with CNV Detection
Stargardt disease (STGD), Fundus Flavimaculatus (FFM) or Retinal Dystrophy, Early-Onset Severe via the ABCA4 Gene


Genetic Counselors
  • Hamel CP. 2007. Cone rod dystrophies. Orphanet J Rare Dis 1;2:7. PubMed ID: 17270046
  • Hollander AI den, Black A, Bennett J, Cremers FPM. 2010. Lighting a candle in the dark: advances in genetics and gene therapy of recessive retinal dystrophies. Journal of Clinical Investigation 120: 3042–3053. PubMed ID: 20811160
  • Huang L, Zhang Q, Li S, Guan L, Xiao X, Zhang J, Jia X, Sun W, Zhu Z, Gao Y, Yin Y, Wang P, et al. 2013. Exome Sequencing of 47 Chinese Families with Cone-Rod Dystrophy: Mutations in 25 Known Causative Genes. PLoS ONE 8: e65546. PubMed ID: 23776498
  • Human Gene Mutation Database (Bio-base).
  • Kohl S, Kitiratschky V, Papke M, Schaich S, Sauer A, Wissinger B. 2012. Genes and mutations in autosomal dominant cone and cone-rod dystrophy. Adv. Exp. Med. Biol. 723: 337–343. PubMed ID: 22183351
  • Sung C-H, Chuang J-Z. 2010. Review series: The cell biology of vision. The Journal of Cell Biology 190: 953–963. PubMed ID: 20855501
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NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most 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 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.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

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.
  • 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.


(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.


(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.


(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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