A seven-year-old female patient with clinical manifestations of PCG referred to us [Table 1] to receive genetic counseling and molecular testing.
The subject was born of consanguineous marriage [Figure 1a]. All family members received genetic counseling, and informed consent was obtained from her parents for participation in the study and publishing the results. We conducted the targeted sequence analysis for the genes associated with PCG (ASB10, CYP1B1, FOXC1, LTBP2, TEK, MYOC, NTF4, OPA1, OPTN, TBK1, and WDR36). Accordingly, we identified a homozygous single base pair deletion in exon 3 of the CYP1B1 gene in reverse strand of genomic position as follows:
(chr2:38298398_38298398delC) (NM_00010 4(CYP1B1):c. 1099_1099delG), p.(D367Tfs*61) [Figure 1b].
This variant is theoretically predicted as a disease-causing factor by Sorting Intolerant From Tolerant (SIFT) (https://sift.bii.a-star.edu.sg/), Protein Variation Effect Analyzer.
(PROVEAN) (http://provean.jcvi.org/index.php), and MutationTaster (http://www.mutationtaster.org/) software and classified as very strong pathogenic (PVS1) null variant according to the ACMG guidelines and standards. This variant is also absent from the 1000 genomes (http://browser. 1000genomes.org/index.html), ExAC browser (http://exac.broadinstitute.org/), Exome Variant Server (EVS) (http://evs.gs.washington. edu/EVS/), and Iranome databases (http://www.iranome.com/). This deletion variant may lead to a frameshift in the translation process, causing the conversion of an amino acid at the position of 367 into the threonine residue. This procedure is probably followed by the emergence of a stop-codon located at 61 codons downstream of the mutation position p.(Asp367Thrfs*61). The Sanger sequencing and segregation analysis confirmed homozygosity of the variant in the patient, while her parents were heterozygote [Figure 1a and b].
The prediction of the 3D structure of the mutated form of the CYP1B1 protein was conducted by the Phyre 2 web portal.
(http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and then visualized by the Yet Another Scientific Artificial Reality Application (YASARA) view software (http://www. yasara.org/viewdl.html). The results of the 3D structure prediction for both mutant and wild-type forms of the CYP1B1 protein revealed that some features might be affected in the mutant form of the protein [Figure 2a and b].
It was also demonstrated that several protein features of the mutant form of CYP1B1 would be lost in each output pairwise alignment when compared with its reference alignment [Figure 2c]. These data were consistent with the stereochemistry analysis obtained from the COACH server, COFACTOR server, and PSIPRED workbench [Table 2].