Cataract 9, Multiple Types (CTRCT9) via the CRYAA Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2901 CRYAA$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

The clinical sensitivity of this test may range up to 30%. In India, none of the 100 congenital cataract cases showed causative CRYAA sequence variants (Kumar et al. 2013). In Australia, 25% (1/4) families with autosomal dominant congenital cataract tested positive for disease-causing CRYAA sequence variants (Laurie et al. 2012). In Denmark, 30% (3/10) of families with hereditary congenital cataract harbored pathogenic sequence variants in the CRYAA gene (Hansen et al. 2007).

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Clinical Features

Cataract 9, multiple types (CTRCT9) is a common congenital, progressive vision disorder that causes blindness in infants (Litt et al. 1998). It is characterized by the development of blurred and dimmed vision resulting from clouding of the lens (opacification) due to changes in its microarchitecture (Kumar et al. 2013). This particular damage to the lens induces light to scatter as well as proteins to aggregate, thereby resulting in loss of transparency (Hejtmancik 2008). CTRCT9 comprises multiple types of cataracts, which mainly depend on the location within the lens, density or opacity, color, symmetry, and progression (Beby et al. 2007; Shafie et al. 2006). Intrafamilial variability in the morphology and location within the lens commonly occurs in CTRCT9 (Javadiyan et al. 2016). The incidence of congenital cataract has been estimated to be roughly 2.5 per 10,000 live births (Wirth et al. 2002; Yi et al. 2011). Perinatal ocular examination in newborns via red reflex examination is generally conducted using an ophthalmoscope (American Academy of Pediatrics 2002), whereas young children are assessed by slit-lamp microscopy (Li et al. 2013). Congenital cataract is usually treated by surgery and early primary intraocular lens implantation during the first year of life (Ventura et al. 2013).


CTRCT9 is an autosomal dominant vision disorder that is caused by pathogenic sequence variants in the crystallin, alpha-a (CRYAA) gene [also known as the crystallin, alpha-1 (CRYA1) and heat-shock protein beta-4 (HSPB4) gene], which is located on chromosome 21q22.3 (Quax-Jeuken et al. 1985). The CRYAA gene consists of three coding exons that encode a 173-amino acid structural protein called alpha-crystallin that protects lens fiber cells from heat-induced necrosis, as well as facilitates in the maintenance of lens transparency. Animal studies using mouse models have shown that alpha-crystallins assist in the normal embryologic development of the anterior segment of the eye. Targeted disruption of the CRYAA gene results in the development of cataracts and the accumulation of cytoplasmic bodies consisting of alpha-B-cystallins. These findings suggest that the CRYAA protein interacts with the crystallin, alpha-b protein as a molecular chaperone to maintain protein solubility, which, when disrupted, results in lens opacity leading to the formation of cataracts (Brady et al. 1997; Graw et al. 2001; Fu and Liang 2002, 2003; Hsu et al. 2006). To date, a total of about 15 pathogenic CRYAA sequence variants have been reported. These variants are mostly missense, small in-frame deletions, and only a few chain termination (nonsense) variants (Human Gene Mutation Database). It has been hypothesized that the missense variants result in changes in charge dispersion at the surface of the CRYAA protein, which is critical for chaperone action and stability (Litt et al. 1998; Mackay et al. 2003; Graw et al. 2001; Vanita et al. 2006; Santhiya et al. 2006).

Testing Strategy

This test involves bidirectional DNA Sanger sequencing of all coding exons of the CRYAA gene. The full coding region of each exon plus ~10 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

Indications for Test

The ideal CRYAA test candidates are individuals who present with congenital, autosomal dominant cataract.


Official Gene Symbol OMIM ID
CRYAA 123580
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Cataract 9 AD 604219

Related Test

Congenital Cataracts Sequencing Panel


Genetic Counselors
  • American Academy of Pediatrics. 2002. Pediatrics. 109: 980-1. PubMed ID: 11986467
  • Beby F. et al. 2007. Archives of Ophthalmology (chicago, Ill. : 1960). 125: 213-6. PubMed ID: 17296897
  • Brady JP. et al. 1997. Proceedings of the National Academy of Sciences of the United States of America. 94: 884-9. PubMed ID: 9023351
  • Fu L., Liang JJ. 2002. The Journal of Biological Chemistry. 277: 4255-60. PubMed ID: 11700327
  • Fu L., Liang JJ. 2003. Investigative Ophthalmology & Visual Science. 44: 1155-9. PubMed ID: 12601044
  • Graw Jochen et al. 2001. Investigative Ophthalmology & Visual Science. 42: 2909–2915. PubMed ID: 11687536
  • Hansen L. et al. 2007. Investigative Ophthalmology & Visual Science. 48: 3937-44. PubMed ID: 17724170
  • Hejtmancik J.F. 2008. Seminars in cell & developmental biology. 19: 134-49. PubMed ID: 18035564
  • Hsu CD. et al. 2006. Investigative Ophthalmology & Visual Science. 47: 2036-44. PubMed ID: 16639013
  • Human Gene Mutation Database (Bio-base).
  • Javadiyan S. et al. 2016. Bmc Research Notes. 9: 83. PubMed ID: 26867756
  • Kumar M. et al. 2013. Molecular Vision. 19: 2436-50. PubMed ID: 24319337
  • Laurie KJ. et al. 2013. Human Mutation. 34: 435-8. PubMed ID: 23255486
  • Li LH. et al. 2013. The British Journal of Ophthalmology. 97: 588-91. PubMed ID: 23426739
  • Litt M. et al. 1998. Human Molecular Genetics. 7: 471-4. PubMed ID: 9467006
  • Mackay DS. et al. 2003. European Journal of Human Genetics : Ejhg. 11: 784-93. PubMed ID: 14512969
  • Quax-Jeuken Y. et al. 1985. Proceedings of the National Academy of Sciences of the United States of America. 82: 5819-23. PubMed ID: 3862098
  • Santhiya ST. et al. 2006. Molecular Vision. 12: 768-73. PubMed ID: 16862070
  • Shafie SM. et al. 2006. American Journal of Ophthalmology. 141: 750-2. PubMed ID: 16564818
  • Vanita V. et al. 2006. Molecular Vision. 12: 518-22. PubMed ID: 16735993
  • Ventura MC. et al. 2013. Arquivos Brasileiros De Oftalmologia. 76: 240-3. PubMed ID: 24061837
  • Wirth MG. et al. 2002. The British Journal of Ophthalmology. 86: 782-6. PubMed ID: 12084750
  • Yi J. et al. 2011. International Journal of Ophthalmology. 4: 422-32. PubMed ID: 22553694
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  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 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 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 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

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 10 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.

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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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