Cataract Panel

PLUSbpg-method Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 3–4 weeks. SEQbpg-method Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 3–4 weeks. DEL/DUPbpg-method Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 3–4 weeks.

Test code: OP0201

The Blueprint Genetics Cataract Panel is a 54 gene test for genetic diagnostics of patients with clinical suspicion of cataract.

The panel covers genes associated with congenital cataract and syndromes in which cataract is accompanied with systemic disease.

About Cataract

Cataract is defined as opacification of the normally transparent crystalline lens. Cataract can be classified as congenital, infantile, juvenile, presenile and senile. Congenital cataract (CC) is present at birth or during early childhood and is one of the most common ocular diseases causing visual impairment or blindness in children worldwide. Nuclear cataract is the most common type of hereditary CC and is characterized by the opacification limited to the embryonic and/or fetal nuclei of the lens (PMID: 24384146). It can be inherited in an autosomal dominant, autosomal recessive or X-linked manner, of which autosomal dominant mode is the most common. Nuclear CC is genetically highly heterogenous. Mutations in lens crystallins (CRYAA, CRYAB, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD) explain approximately half of the cases, followed by connexins (GJA3, GJA8). Congenital nuclear cataract can be isolated (70% of cases) or accompanied with other ocular disorders, such as microphthalmia or aniridia. It may also be part of multisystem genetic disorders such as Nance–Horan syndrome (NHS), Lowe syndrome (OCRL) or neurofibromatosis type 2 (NF2). The prevalence of cataract in children has been estimated between 1-15:10,000.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

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Genes in the Cataract Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
ABCB6 Blood group, Langereis system, Pseudohyperkalemia AD/BG 9 57
ADAMTSL4 Ectopia lentis, isolated AR 7 20
AGK* Sengers syndrome AR 16 19
ALDH18A1 Spastic paraplegia, Cutis laxa AD/AR 18 25
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 22 44
BFSP2 Cataract AD/AR 2 7
COL2A1 Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1 AD 106 537
COL4A1 Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel disease AD 27 88
COL11A1 Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2 AD/AR 18 76
COL18A1 Knobloch syndrome AR 13 29
CRYAA Cataract AD/AR 10 20
CRYAB Cataract, myofibrillar myopathy and cardiomyopathy, Congenital cataract and cardiomyopathy, Dilated cardiomyopathy (DCM), Myopathy, myofibrillar AD 14 25
CRYBB1 Cataract AD/AR 3 13
CRYBB2* Cataract AD 6 22
CRYBB3 Cataract AR 3 7
CRYGC Cataract AD 9 18
CRYGD Cataract AD 9 25
CYP27A1 Cerebrotendinous xanthomatosis AR 55 99
ERCC2 Xeroderma pigmentosum, Trichothiodystrophy, photosensitive AR 18 90
ERCC5 Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndrome AR 17 51
ERCC6 Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndrome AD/AR 37 91
ERCC8 UV-sensitive syndrome, Cockayne syndrome AR 9 39
EYA1 Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome AD 33 186
FAM126A Leukodystrophy, hypomyelinating AR 6 12
FOXE3 Aphakia, congenital primary, Anterior segment mesenchymal dysgenesis AR/AD 3 21
FTL Hyperferritinemia-cataract syndrome, L-ferritin deficiency, Neurodegeneration with brain iron accumulation AD/AR 20 61
FYCO1 Cataract AR 6 13
FZD4 Retinopathy of prematurity, Exudative vitreoretinopathy AD/Digenic 9 85
GALK1 Galactokinase deficiency AR 6 38
GALT Galactosemia AR 239 319
GCNT2 Blood group, Ii, Adult i pheno without cataract, Cataract 13 with adult i pheno BG/AR 7 12
GJA1* Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3 AD 23 103
GJA3 Cataract AD 12 38
GJA8 Cataract AD/AR 15 50
HSF4 Cataract AD 4 16
LIM2 Cataract AR 2 3
MAF Ayme-Gripp syndrome AD 16 16
MYH9 Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness AD 19 113
NDP Exudative vitreoretinopathy, Norrie disease XL 25 155
NF2 Schwannomatosis, Neurofibromatosis AD 24 423
NHS Nance-Horan syndrome, Cataract XL 19 43
OCRL Lowe syndrome, Dent disease XL 33 251
OPA3 Optic atrophy, 3-methylglutaconic aciduria AD/AR 7 12
PAX6 Aniridia, cerebellar ataxia, and mental retardation (Gillespie syndrome), Keratitis, Coloboma, ocular, Cataract with late-onset corneal dystrophy, Morning glory disc anomaly, Foveal hypoplasia, Aniridia, Optic nerve hypoplasia, Peters anomaly AD 49 461
PITX3 Cataract, Anterior segment mesenchymal dysgenesis AD 3 12
RAB3GAP1 Warburg micro syndrome AR 16 58
RECQL4 Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndrome AR 34 92
SIL1 Marinesco-Sjogren syndrome AR 14 49
SLC33A1* Congenital cataracts, hearing loss, and neurodegeneration AR 6 7
TDRD7 Cataract AR 1 3
TFAP2A Branchiooculofacial sydrome AD 9 42
TMEM70 Mitochondrial complex V (ATP synthase) deficiency AR 9 18
WFS1 Wolfram syndrome, Deafness AD/AR 59 343
WRN* Werner syndrome AR 20 97

*Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Gene Genomic location HG19 HGVS RefSeq RS-number Comment Reference
COL11A1 Chr1:103491958 c.781-450T>G NM_080629.2 rs587782990
ERCC6 Chr10:50681659 c.2599-26A>G NM_000124.3 rs4253196
FTL Chr19:49468616 c.-149G>C NM_000146.3 rs398124638
FTL Chr19:49468606 c.-159G>C NM_000146.3 rs398124634
FTL Chr19:49468605 c.-160A>G NM_000146.3 rs398124633
FTL Chr19:49468604 c.-161C>T NM_000146.3 rs398124636
FTL Chr19:49468601 c.-164C>A/T NM_000146.3 rs398124637
FTL Chr19:49468597 c.-168G>A/C/T NM_000146.3 rs398124635
FTL Chr19:49468586 c.-175_-170delGTCTCT NM_000146.3 rs398124639
FTL Chr19:49468587 c.-178T>G NM_000146.3
FTL Chr19:49468583 c.-182C>T NM_000146.3
GALT Chr9:34649617 c.1059+56C>T NM_000155.3 rs111033821
OCRL ChrX:128687279 c.239-4023A>G NM_000276.3
PAX6 Chr11:31832374 c.-129+2T>A NM_000280.4
WRN Chr8:30966107 c.2089-3024A>G NM_000553.4 rs281865157

Blueprint Genetics offers a comprehensive Cataract Panel that covers classical genes associated with COFS syndrome, cataract, cataract-microcornea syndrome, early-onset non-syndromic cataract, hereditary hyperferritinemia with congenital cataracts, Marinesco-Sjogren syndrome, Nance-Horan syndrome and oculocerebrorenal syndrome. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Cataract Panel

ICD-10 Disease
Q12.0 Cataract

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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