December 8, 2022
Human vision relies on two types of photoreceptor cells: rods and cones. Rods are responsible for vision under low-light conditions, and cones are responsible for day-light vision and color perception. Cones can be further distinguished into three classes, and any alteration in a cone class can lead to color blindness (1). However, if all three cones are non-functional it leads to achromatopsia, which is an inability to see clearly in bright light, poor visual acuity, and color blindness (2).
Achromatopsia is an autosomal recessive and rare condition, with a frequency of 1 in 30,000 live births worldwide. There are a few genetic causes of achromatopsia, and one involves cyclic nucleotide-gated ion channels (CNGB3). Few mutations in CNGB3 have been characterized for achromatopsia, and the majority of these mutations are loss of function resulting in a truncated protein. Achromatopsia is typically diagnosed around six months of age due to intolerance to the perception of light (photophobia) and involuntary eye movement (nystagmus)(2).
A clinical geneticist team at the Hadassah Medical Center, Jerusalem, has been analyzing thousands of rare genetic disorders during the last decade and strives to provide accurate diagnoses to patients and their families. With their current platform, they achieve a diagnostic yield of approximately 50%, and for the remaining undiagnosed cases, they choose to implement Geneyx Analysis. One complex case they encountered was a female of Ethiopian descent that was diagnosed with achromatopsia. To confirm the clinical diagnosis, next-generation sequencing was performed. The fastq files were processed using the secondary pipeline integrated with Geneyx, and the VCF files were then annotated and analyzed using Geneyx Analysis.
Achromatopsia was entered in the phenotyper and resulted in a highly prioritized variant in the CNGB3 gene (Figure 1). Using the FastTrack filter logic, the variant displayed as the first candidate among 62,000 variants. The zygosity for this variant was homozygous in the autosomal recessive CNGB3 gene, and the ACMG classification showed a likely pathogenic finding. Of interest, this variant was a splice site donor near exon 9 of the CNGB3 gene but showed a low coverage profile upon BAM visualization. Further investigation was made to understand if this mutation was the result of a compound heterozygous mutation due to an overlapping CNV.
Figure 1: CNGB3 displayed as the candidate variant with achromatopsia used for phenotypic prioritization.
CNV analysis in Geneyx resulted in identifying a heterozygous deletion event that overlapped two exons of the CNGB3 gene. According to ClinVar, this event has been classified as pathogenic and was rare in control databases. This event was characterized by a high-quality score indicating that the significant reduction in coverage over this region was due to a deletion event. Furthermore, this confirmed an overlap with the splice site mutation in the CNGB3 gene, resulting in a compound heterozygous mutation (Figure 2).
Figure 2: Coverage profile for exon 9 of the CNGB3 gene shows deletion event overlapping with the splice site intronic variant, resulting in a compound heterozygous mutation.
In this case study, Geneyx Analysis was able to identify a rare compound heterozygous mutation associated with achromatopsia. Using phenotypic prioritization, the candidate variant was quickly identified and allowed the investigator to pursue a deeper understanding of the genetic profile. CNV analysis discovered an overlapping heterozygous deletion, which then characterized the causal finding as a compound heterozygous mutation of the CNGB3. In summary, Geneyx Analysis is a leading variant analysis and interpretation platform that can handle complex cases, including compound mutations of CNVs and SNVs. For this reason, the Hadassah Medical Center in Jerusalem, and other hospitals worldwide, are able to continue to identify rare mutations using Geneyx Analysis and improve diagnostic yields and improve patient care.