- Is a 76 gene panel that includes assessment of non-coding variants
Is ideal for patients with a clinical suspicion / diagnosis of congenital cataracts or a syndrome with cataracts as a feature.
The Blueprint Genetics Cataract Panel (test code OP0201):
Commonly used ICD-10 code(s) when ordering the Cataract Panel
|Q12.0||Early-onset non-syndromic cataract|
|H26.009||Hereditary hyperferritinemia with congenital cataracts|
- Blood (min. 1ml) in an EDTA tube
- Extracted DNA, min. 2 μg in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)
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. Read more about our sample requirements here.
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 the autosomal dominant mode is the most common. Nuclear CC is genetically highly heterogeneous. 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%) or associated 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.
Genes in the Cataract Panel and their clinical significance
|ABCB6||Blood group, Langereis system, Pseudohyperkalemia, Dyschromatosis universalis hereditaria, Microphthalmia, isolated, with coloboma 7||AD/BG||9||20|
|ADAMTS18||Knobloch syndrome 2, Microcornea, myopic chorioretinal atrophy, and telecanthus, Retinal dystrophy, early onset, autosomal recessive||AR||4||14|
|ADAMTSL4||Ectopia lentis, isolated||AR||11||27|
|AGK*||Sengers syndrome, Cataract 38||AR||18||27|
|ALDH18A1||Spastic paraplegia, Cutis laxa||AD/AR||22||30|
|BCOR||Microphthalmia, syndromic, Oculofaciocardiodental syndrome||XL||40||53|
|CHMP4B||Cataract 31, multiple types||AD||2||2|
|COL11A1||Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2||AD/AR||34||94|
|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||180||561|
|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||58||107|
|CRYAB||Cataract, myofibrillar myopathy and cardiomyopathy, Congenital cataract and cardiomyopathy, Dilated cardiomyopathy (DCM), Myopathy, myofibrillar, Cataract 16, multiple types, Myopathy, myofibrillar, fatal infantile hypertonic, alpha-B crystallin-related||AD||14||28|
|CRYBA1||Cataract 10, multiple types||AD||9||13|
|CRYGS||Cataract, progressive polymorphic cortical||AD||3||8|
|CTDP1||Congenital cataracts, facial dysmorphism, and neuropathy||AR||1||1|
|EPHA2||Cataract 6, multiple types||AD||7||20|
|ERCC2||Xeroderma pigmentosum, Trichothiodystrophy, photosensitive, Cerebrooculofacioskeletal syndrome 2||AR||26||98|
|ERCC5||Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndrome||AR||21||54|
|ERCC6*||Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndrome||AD/AR||87||135|
|ERCC8||UV-sensitive syndrome, Cockayne syndrome||AR||34||64|
|EYA1||Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome||AD||56||218|
|FOXE3||Aphakia, congenital primary, Anterior segment mesenchymal dysgenesis, Cataract 34, Aortic aneurysm, familial thoracic||AR/AD||9||29|
|FTL||Hyperferritinemia-cataract syndrome, L-ferritin deficiency, Neurodegeneration with brain iron accumulation||AD/AR||21||63|
|FZD4||Retinopathy of prematurity, Exudative vitreoretinopathy||AD/Digenic||14||90|
|GALE||Galactose epimerase deficiency||AR||12||26|
|GCNT2||Blood group, Ii, Adult i pheno without cataract, Cataract 13 with adult i pheno||BG/AR||11||11|
|GJA1*||Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3||AD/AR||31||107|
|LEMD2||Cataract 46, juvenile onset, Arrhythmogenic right ventricular cardiomyopathy (ARVC), Dilated cardiomyopathy (DCM)||AR||1||1|
|MAF#||Ayme-Gripp syndrome, Cataract 21, multiple types||AD||21||22|
|MIP||Cataract 15, multiple types||AD||11||27|
|MYH9||Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness, Deafness, autosomal dominant 17||AD||25||117|
|NDP||Exudative vitreoretinopathy, Norrie disease||XL||31||167|
|NHS||Nance-Horan syndrome, Cataract||XL||36||52|
|OCRL||Lowe syndrome, Dent disease||XL||47||264|
|OPA3||Optic atrophy, 3-methylglutaconic aciduria||AD/AR||13||15|
|P3H2||Myopia, high, with cataract and vitreoretinal degeneration||AR||7||7|
|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||144||550|
|PITX3||Cataract, Anterior segment mesenchymal dysgenesis||AD||5||11|
|PXDN||Anterior segment dysgenesis 7||AR||7||14|
|RAB18||Warburg micro syndrome 3||AR||5||5|
|RAB3GAP1||Warburg micro syndrome||AR||29||66|
|RAB3GAP2||Warburg micro syndrome, Martsolf syndrome||AR||11||15|
|RECQL4||Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndrome||AR||82||114|
|SLC33A1*||Congenital cataracts, hearing loss, and neurodegeneration, Spastic paraplegia 42, autosomal dominant||AD/AR||6||7|
|TBC1D20||Warburg micro syndrome 4||AR||6||6|
|TMEM70||Mitochondrial complex V (ATP synthase) deficiency||AR||12||18|
|VIM||Cataract 30, multiple types||AD||2||3|
|VSX2||Microphthalmia, isolated 2, Microphthalmia, isolated, with coloboma 3||AR||9||13|
|WFS1||Wolfram syndrome, Deafness, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41||AD/AR||69||362|
* Some, or all, of the gene is duplicated in the genome. Read more.
# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).
The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)
Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.
Non-coding variants covered by Cataract Panel
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number|
Added and removed genes from the panel
|Genes added||Genes removed|
|DNMBP LEMD2 RAB18 RAB3GAP2 SIPA1L3 TBC1D20 XYLT2|
- CAP and ISO-15189 accredited laboratory
- CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
- Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
- Careful construction of clinically effective and scientifically justified gene panels
- Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
- Our publicly available analytic validation demonstrating complete details of test performance
- ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see below ‘Non-coding disease causing variants covered by this panel’)
- Our rigorous variant classification scheme
- Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
- Our comprehensive clinical statements
Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).
- Complex inversions
- Gene conversions
- Balanced translocations
- Mitochondrial DNA variants
- Repeat expansion disorders unless specifically mentioned
- Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
- Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- Stretches of mononucleotide repeats
- Indels larger than 50bp
- Single exon deletions or duplications
- Variants within pseudogene regions/duplicated segments
The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.
For additional information, please refer to the Test performance section and see our Analytic Validation.
The Blueprint Genetics cataract panel covers classical genes associated with cataract, early-onset non-syndromic cataract, Oculocerebrorenal syndrome, Nance-Horan syndrome, Marinesco-Sjogren syndrome, COFS syndrome, Cataract-microcornea syndrome and hereditary hyperferritinemia with congenital cataracts. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.
Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).
Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.
Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.
|Sensitivity % (TP/(TP+FN)||Specificity %|
|Single nucleotide variants||99.89% (99,153/99,266)||>99.9999|
|Insertions, deletions and indels by sequence analysis|
|1-10 bps||96.9% (7,563/7,806)||>99.9999|
|11-50 bps||99.13% (2,524/2,546)||>99.9999|
|Copy number variants (exon level dels/dups)|
|1 exon level deletion (heterozygous)||100% (20/20)||NA|
|1 exon level deletion (homozygous)||100% (5/5)||NA|
|1 exon level deletion (het or homo)||100% (25/25)||NA|
|2-7 exon level deletion (het or homo)||100% (44/44)||NA|
|1-9 exon level duplication (het or homo)||75% (6/8)||NA|
|Simulated CNV detection|
|5 exons level deletion/duplication||98.7%||100.00%|
|Microdeletion/-duplication sdrs (large CNVs, n=37))|
|Size range (0.1-47 Mb)||100% (37/37)|
|The performance presented above reached by WES with the following coverage metrics|
|Mean sequencing depth at exome level||143X|
|Nucleotides with >20x sequencing coverage (%)||99.86%|
The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. 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. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.
We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.
Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.
The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call. Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.
Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.
Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.
Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.