Congenital Stationary Night Blindness Panel

Updated
Summary
  • Is a 20 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion / diagnosis of congenital stationary night blindness. The genes on this panel are included in the Retinal Dystrophy Panel.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

20

Test code

OP1201

Panel size

Small

CPT codes
81479

Summary

The Blueprint Genetics Congenital Stationary Night Blindness Panel (test code OP1201):

Test Specific Strength

This panel covers genes associated with autosomal dominant, autosomal recessive and X-linked congenital stationary night blindness (CSNB). The clinical utility of this panel is very high (almost 100%) for patients with X-linked CSNB.

ICD codes

Commonly used ICD-10 code(s) when ordering the Congenital Stationary Night Blindness Panel

ICD-10 Disease
H53.60 Oguchi disease
H53.60 Congenital stationary night blindness

Sample Requirements

  • 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.

Please include fundus photographs, electroretinogram (ERG) findings, visual field findings and visual acuity, if available, for expert review and clinical correlation with test results

Congenital stationary night blindness (CSNB) is a non-progressive retinal disorder that is characterized by night or dim light vision disturbance or delayed dark adaptation, poor visual acuity (ranging from 20/30 to 20/200), myopia, nystagmus, strabismus, normal color vision and fundus abnormalities. CSNB can be subdivided according to the pattern of inheritance which may be X-linked, autosomal recessive or autosomal dominant. X-linked CSNB accounts for 57.9% of cases, autosomal recessive and sporadic CSNB account for 40% including 23.6% with a fundus abnormality, and the remaining 2.1% of cases have autosomal dominant CSNB. The incomplete form of X-linked CSNB (CSNB2) is caused by mutations in the CACNA1F gene and the complete form of X-linked CSNB (CSNB1) is due to defects in the NYX gene. Oguchi disease is a rare autosomal recessive form of CSNB associated with fundus discoloration and abnormally slow dark adaptation.

Genes in the Congenital Stationary Night Blindness Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
CABP4 Night blindness, congenital stationary AR 6 11
CACNA1F Aland Island eye disease, Cone rod dystrophy, Night blindness, congenital stationary XL 39 182
CACNA2D4 Retinal cone dystrophy AR 3 9
CYP4V2 Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophy AR 31 94
FRMD7 Nystagmus, infantile periodic alternating XL 15 95
GNAT1 Night blindness, congenital stationary AD/AR 5 10
GNB3 Night blindness, congenital stationary, type 1H AR 3 6
GPR179 Night blindness, congenital stationary AR 13 16
GRK1 Oguchi disease AR 5 23
GRM6 Night blindness, congenital stationary AR 11 38
LRIT3 Night blindness, congenital stationary AR 4 9
NYX Night blindness, congenital stationary XL 12 89
PDE6B Retinitis pigmentosa, Night blindness, congenital stationary AD/AR 35 125
RDH5 Fundus albipunctatus AR 11 51
RHO Retinitis pigmentosa, Night blindness, congenital stationary, Retinitis punctata albescens AD/AR 58 212
RLBP1 Newfoundland rod-cone dystrophy, Fundus albipunctatus, Bothnia retinal dystrophy, Retinitis punctata albescens AR 9 37
RPE65 Retinitis pigmentosa, Leber congenital amaurosis AR 31 197
SAG Retinitis pigmentosa, Oguchi disease AD/AR 6 15
SLC24A1 Night blindness, congenital stationary, type 1D AR 7 26
TRPM1 Night blindness, congenital stationary AR 21 82

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 Congenital Stationary Night Blindness Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
FRMD7 ChrX:131228285 c.285-118C>T NM_194277.2
RDH5 Chr12:56114302 c.-33+2dupT NM_002905.3
RPE65 Chr1:68910577 c.246-11A>G NM_000329.2

Added and removed genes from the panel

Genes added Genes removed
FRMD7
GRK1

Test Strengths

This panel covers genes associated with autosomal dominant, autosomal recessive and X-linked congenital stationary night blindness (CSNB). The clinical utility of this panel is very high (almost 100%) for patients with X-linked CSNB.

The strengths of this test include:
  • 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

Test Limitations

This test does not detect the following:
  • 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).
This test may not reliably detect the following:
  • 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 congenital stationary night blindness panel covers classical genes associated with Oguchi disease and congenital stationary night blindness. 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%

Bioinformatics

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.

Clinical interpretation

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.

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