Mohammad Miryounesi

Mitochondrial diseases, often stemming from recessive nuclear gene mutations, represent a heterogeneous group of disorders with significant morbidity and mortality. Carrier screening for these conditions is population-specific, yet data on the pathogenic variant burden in the Iranian population remain limited. This study aimed to analyze whole-exome sequencing (WES) data from 9989 Iranian individuals to identify the spectrum and frequency of recessive mitochondrial disease variants and to develop a population-specific carrier screening panel. We analyzed WES data from 9989 unrelated Iranian individuals. Variants in 1,564 nuclear genes associated with mitochondrial function were filtered for rarity (minor allele frequency < 0.01 in public databases), predicted pathogenicity, and recessive inheritance patterns (homozygous or compound heterozygous). Clinically relevant variants were manually curated, and carrier frequencies for significant recessive mitochondrial conditions were calculated. Our analysis identified variants across 15 groups of mitochondrial-related nuclear genes in 345 individuals recognized as carriers. Of these, 123 variants (35.6%) were classified as Pathogenic, and 154 variants (44.6%) were classified as Likely Pathogenic according to ACMG guidelines. This study provides the first large-scale WES-derived assessment of recessive mitochondrial disease carrier burden in the Iranian population. The high estimated carrier rate supports implementing population-specific preconception screening. The results of this study can be used for design of targeted panels of nuclear mitochondrial genes to identify at-risk couples, facilitating genetic counseling and reproductive decision-making in Iran.

Krabbe disease (KD, OMIM #245200) is a rare autosomal recessive lysosomal storage disorder characterized by severe demyelination affecting both the central

Leukodystrophies are a number of rare genetic disorders that influence the white matter of the brain. The current study aimed to identify the underlying genetic cause of leukodystrophy in 14 Iranian cases, mainly presented by hypomyelinating leukodystrophies. Whole exome sequencing was used for this purpose. Notably, a certain RARS1 variant (c.2T > C) was found in six cases. In addition, six cases carried homozygote variants in the GJC2, PLEKHG2, RNF220, POLR1C, DEGS1 and ACER3 genes, respectively. Finally, two patients carried a heterozygote variant in TMEM63A or TUBB4A, respectively. Taken together, the current study shows high prevalence of a certain RARS1 variant among Iranian patients with leukodystrophy. Moreover, a list of other genes was suggested as underlying causes of leukodystrophy in this population. Further studies are needed to elaborate the spectrum of genetic mutations in Iranian cases with leukodystrophy.

Kabuki Syndrome (KS) is a rare, multisystem congenital disorder with five foremost clinical manifestations encompassing dysmorphic facial characteristics, postnatal growth constraint, craniofacial/skeletal anomalies, mild to moderate intellectual disability, and dermatoglyphic abnormalities. We analyzed two unrelated Iranian patients suspected of having KS using whole-exome sequencing. An in silico analysis was performed to evaluate the potential effects of the discovered variants on the structure and function of the corresponding protein. A novel de novo heterozygous protein-truncating mutation was found in patient 1, NM_003482.4: c.13818C>G (p.Y4606X), and a de novo heterozygous premature stop codon was identified in patient 2, NM_003482.4: c.16360C>T (p.R5454X). These mutations cause haploinsufficiency in KMT2D and are absent in the proband’s parents. Although these mutations provide evidence of the potential pathogenicity of KMT2D in KS, further functional studies are necessary to confirm their impact. Our observations not only provide evidence for the potential pathogenicity of the two identified protein-truncating mutations but also have important implications for the accurate diagnosis and potential treatment of KS. These findings underscore the significance of genetic testing in diagnosing this disorder and expand our understanding of the role of KMT2D mutations in its pathogenesis.

Limb–girdle muscular dystrophies (LGMD) designate diverse types of muscular dystrophies that predominantly affect proximal skeletal muscles. Although both autosomal recessive and dominant forms exist, the majority of cases are inherited in an autosomal recessive manner. Since the spectrum of genetic variants that cause this disorder is quite broad, next-generation sequencing techniques are the best diagnostic tools for LGMD. In this study, we provide an overview of mutation spectrum of LGMD-related genes in the Iranian patients using whole exome sequencing. Notably, CAPN3 and LAMA2 genes were the genes encompassing the highest frequencies of pathogenic or likely pathogenic variants in this cohort. Pathogenic and likely pathogenic variants were identified in CAPN3 gene in total of 10 cases out of 48 cases tested (20%). In addition, different variants in each of POMGNT1 and TTN genes were detected in five and four patients, respectively. Three patients had DYSF variants (6%). While the inheritance of the majority of cases was supposed to be in an autosomal recessive manner, in three cases, the disease inheritance was best explained by the dominant type (c.947 C > T variant in the DNAJB6, c.746G > A variant in the LMNA, and c.1417G > A variant in the TNPO3). The current study broadens the spectrum of LGMD-related mutations among Iranian patients and facilitates genetic counseling in the affected families.

Methylmalonic aciduria (MMA) is described by high methylmalonic acid concentrations in the blood and urine. This condition can be isolated or in combination with homocystinuria. While variants in the MMUT, MMAA, MMAB, MMADHC and MCEE genes contribute to the pathogenesis of the isolated form, variants in MMACHC, MMADHC, LMBRD1, and ABCD4 genes, are responsible for diverse types of combined MMA and homocystinuria. In the current study, we report molecular tests of 15 Iranian patients who had mutations in MMA-related genes. Among the assessed patients, MMACHC gene was the most prevalently mutated gene (mutated in 7 patients). Each of MMAA, MMAB, and MMUT genes were mutated in 2 patients, respectively. Finally, we detected variants in each of ACSF3 and ABCD4 genes in one case, respectively. Among the identified variants, five variants were not reported before. Cumulatively, the current study provides some data about MMA-related variants among Iranian patients.

Bardet–Biedl syndrome (BBS, OMIM 209900) is a rare autosomal recessive disorder characterized by a broad spectrum of clinical features including renal anomalies, learning disabilities, postaxial polydactyly, retinal dystrophy, obesity, and hypogonadism. BBS is a heterogeneous syndrome, both genetically and clinically. To date, genetic variants in more than 28 genes have been associated with this syndrome and its subtypes. Most previous studies on BBS have failed to show clear genotype–phenotype correlations. In order to investigate the spectrum of genetic variation among Iranian BBS patients, 9 subjects from 9 different families with clinically diagnosed BBS were included in this study. Following informed consent, we applied exome sequencing (ES) to the proband and their parents. We next performed Sanger sequencing to validate the identified variants. ES successfully detected four known variants: two in the BBS9 gene, c.2014C > T (p.Gln672Ter) and c.1789 + 1 G > A, one variant in the BBS10 gene (c.728_731del; p.Lys243Ilefs*15), and one variant in the MKKS gene (c.515_516del; p.Glu172Alafs*19). ES also detected two new variants in the BBS7 gene, c.880G > C (p.Gly294Arg) and c.719G > A (p.Gly240Asp), one new variant in the CEP290 gene, c.5159C > G (p.Thr1720Arg), and one new variant, in the TTC8 gene, c.462_465del (p.Ser155Glufs*20). In addition, ES identified one novel homozygous deletion of exon 16 in the BBS9 gene. Among the clinical manifestations observed, obesity and polydactyly were the most common findings. Our findings further support the high heterogeneity of BBS: by discovering known, new, and novel pathogenic variants. We expand the mutational spectrum of BBS-related genes and contribute to the understanding of this multisystem disease.

Knobloch Syndrome (KS) is a rare genetic disorder characterized by ocular abnormalities and central nervous system (CNS) defects, which are attributed to collagenopathy. The primary gene implicated in KS is COL18A1, which encodes the alpha chain of type XVIII collagen. This type of collagen functions as a proteoglycan, predominantly located in the basement membrane of human tissues. This study examined an Iranian female presenting with symptoms of horizontal nystagmus, strabismus, and suspected vision loss, with a potential diagnosis of KS. Genomic DNA was subjected to whole-exome sequencing (WES). The identified pathogenic variant was subsequently confirmed using Sanger sequencing. The impact of the identified pathogenic variant on the structure of COL18A1 was assessed using I-TASSER. Analysis of WES data revealed two pathogenic compound heterozygous variants, c.2416C>T (p.Arg806Ter) and c.1698delC (p.Gly567AspfsTer45), in exons 7 and 16, respectively, of the COL18A1 (NM_030582) gene. Furthermore, a standard literature review of clinical data highlighted the heterogeneity of phenotypic manifestations, ranging from mild ocular abnormalities to severe neurodevelopmental impairments. This study and literature search offer valuable insights into the genetic landscape of KS, thereby expanding our understanding of the disease and its clinical implications. The identification of novel variants in key genes sheds light on the underlying molecular mechanisms and potential therapeutic targets.