• Test code: 05132
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit

Invitae Congenital Cataracts Panel

Test description

The Invitae Congenital Cataracts Panel analyzes up to 38 genes that are associated with congenital cataracts, a condition characterized by lens opacity. These genes were curated based on the available evidence to date to provide a comprehensive analysis for inherited congenital cataracts. The genetic heterogeneity associated with congenital cataracts can make it difficult to use phenotype as the sole criterion to select a definitive cause. Comprehensive panel testing allows for an efficient evaluation of several potential genes based on a single clinical indication.

Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant can inform recurrence-risk assessment and genetic counseling.

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Primary panel (34 genes)


Add-on Preliminary-evidence Genes for Congenital Cataracts (4 genes)

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.


  • aniridia
  • Axenfeld-Rieger syndrome
    • Axenfeld-Rieger syndrome type 1
    • Axenfeld-Rieger syndrome type 3
  • Ayme-Gripp syndrome
  • cataracts
    • cataract types 1-6, 9-12, 14-18, 20-22, 33, 40
    • cataract, syndromic 11
    • cataract 13 with adult i phenotype
    • cataract with late-onset corneal dystrophy
    • congenital cataracts, facial dysmorphism, and neuropathy
    • galactokinase deficiency with cataracts
    • hypomyelination and congenital cataract type 5
  • Dent disease 2
  • foveal hypoplasia 1
  • Gillespie syndrome
  • iridogoniodysgenesis type 1
  • iris hypoplasia and glaucoma
  • keratitis
  • Lowe syndrome
  • Marinesco-Sjogren syndrome
  • microphthalmia
    • microphthalmia, syndromic 2
    • microphthalmia with coloboma 3
    • microphthalmia, isolated 2
  • Nance-Horan syndrome
  • optic nerve hypoplasia
  • Peters anomaly
  • Sengers syndrome

Bilateral congenital cataracts are the most common cause of treatable childhood blindness worldwide and are characterized by opacification of the lens. About 70% of individuals with congenital cataracts have abnormalities that are restricted to the lens, while 15% have additional eye findings and 15% have a multisystemic syndrome. Between a quarter and a third of congenital cataracts are believed to be hereditary, and a variety of environmental exposures are known to contribute to their development. The type of cataract is defined by its location in the lens (complete, polar/subcapsular, nuclear, lamellar, sutural, cortical, or membranous/capsular). Pathogenic genetic changes that cause cataracts are located within proteins that are important to maintain cell transparency and homeostasis. They are most commonly found within crystallins and connexins but can also occur in enzymes and in growth and transcription factors as well as in cytoskeletal, membranous, and cell-signaling proteins.

Based on the currently available publications, whose sample sizes are limited, the sensitivity of this panel is expected to be about 70% or greater for individuals with a clinical diagnosis of congenital cataracts.

Inherited cataracts can occur in several inheritance patterns, including autosomal dominant, autosomal recessive, and X-linked recessive.

Penetrance is generally high. Environmental factors can influence both the penetrance and the clinical heterogeneity of the disorder, particularly for cataracts that show onset after the congenital period.

Bilateral congenital cataracts are the most common cause of treatable childhood blindness, with a prevalence of about 1–6 in 100,000 individuals in industrialized countries. In general, the prevalence of congenital cataracts is lower in industrialized countries than in the poorest regions of the world, where the prevalence is thought to range from 5–15 in 10,000 individuals.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
AGK NM_018238.3
BCOR NM_017745.5
BFSP1 NM_001195.4
BFSP2 NM_003571.3
CHMP4B NM_176812.4
CRYAA NM_000394.3
CRYAB NM_001885.2
CRYBA1 NM_005208.4
CRYBA4 NM_001886.2
CRYBB1 NM_001887.3
CRYBB2 NM_000496.2
CRYBB3 NM_004076.4
CRYGB NM_005210.3
CRYGC NM_020989.3
CRYGD NM_006891.3
CRYGS NM_017541.2
CTDP1* NM_004715.4
EPHA2 NM_004431.3
FAM126A NM_032581.3
FOXC1 NM_001453.2
FYCO1 NM_024513.3
GALK1 NM_000154.1
GCNT2 NM_001491.2
GJA3 NM_021954.3
GJA8 NM_005267.4
HSF4 NM_001538.3
LIM2 NM_030657.3
MAF NM_005360.4
MIP NM_012064.3
NHS NM_198270.3
OCRL NM_000276.3
PAX6 NM_000280.4
PITX2 NM_153427.2
PITX3 NM_005029.3
SIL1 NM_022464.4
TDRD7 NM_014290.2
VIM NM_003380.3
VSX2 NM_182894.2

CTDP1: c.863+389C>T variant only.