Intronic OTOF mutation causes an atypical splicing defect resulting in auditory neuropathy spectrum disorder.

Pathogenic variants in OTOF cause auditory neuropathy spectrum disorder (ANSD), namely prelingual nonsyndromic ANSD and temperature-sensitive ANSD (TS-ANSD). All study subjects provided blood sample for genetic analysis and sequencing. Wholeexome sequencing was carried out to identify the causative pathogenic variant. RNAwas extracted to analyse the messenger RNA (mRNA) resulting from the transcription of OTOF. Here, we identified a family with OTOF-related ANSD. This disorder was caused by an intronic mutation in OTOF (NM_194248: c.2406>4A[G). In further analysis, we proved that this variant causes a splicing defect resulting in the omission of exon 20 from the mRNA transcribed from OTOF. In this study, we demonstrated that the variant is four nucleotides away from the conventional splicing site, and our findings suggest that splicing mechanisms need to be better understood, as well as how neighbouring regions may impact splicing.

A combination of two novels homozygous FCSK variants cause disorder of glycosylation with defective fucosylation: New patient and literature review.

Pathogenic variants in FCSK cause Congenital Disorder of Glycosylation with Defective Fucosylation-2 (FCSK-CDG; MIM: 618,324). It is a rare autosomal recessive genetic disease caused by defects in the L-fucose kinase, which is necessary for the fucose salvage pathway. Herein, we report two novel variants in an Iranian patient, the fourth individual with FCSK-CDG described in the literature. Two homozygous variants in FCSK (rs376941268; NM_145059.3: c.379C > A, p. Leu127Met and rs543223292; NM_145059.3: c.394G > C, p. Asp132His) were identified in the proband. Sanger sequencing conducted on his unaffected parents revealed that they were heterozygous for the same variants. The proband, a four-and-a-half year old Iranian male born to consanguineous parents, manifested Intellectual disability, growth delay, ophthalmic abnormalities, seizures, speech disorder, and feeding difficulties.

MCM2 mutation causes autosomal dominant nonsyndromic hearing loss (DFNA70): novel variant in the second family.

Pathogenic variants in MCM2 could result in mild to severe sensorineural hearing loss in the affected individuals (deafness, autosomal dominant 70; DFNA70; OMIM: 616968), an extremely rare autosomal dominant progressive disorder. Here, we report a novel missense variant (NM_004526:c.388C>T, p.R130C; Clinvar: SCV002072508) in MCM2 in an Iranian family identified by whole-exome sequencing and confirmed by Sanger sequencing. The heterozygous variant (NM_004526:c.388C>T, p.R130C) in MCM2 was identified in the proband and his mother. The proband is a nine-year-old male born to nonconsanguineous parents. The proband was characterized by nonsyndromic hearing loss, while his mother showed a mild form of the disorder. This study reports the second disease-causing variant in MCM2 in the world and confirms that hearing loss arising from variants in MCM2 is nonsyndromic. Nevertheless, as was reported in the previous family, phenotype could vary among the patients with the same variant.

Genotypic and phenotypic spectrum of Myofibrillar Myopathy 7 as a result of Kyphoscoliosis Peptidase deficiency: The first description of a missense mutation in KY and literature review.

KY is located on chromosome 3 and encodes a transglutaminase-like protein in the skeletal muscles, namely Kyphoscoliosis Peptidase. KY is primarily involved in the formation and stabilization of neuromuscular intersections making it essential for the development of the musculoskeletal system. Mutations in KY cause Myofibrillar Myopathy-7 (MFM-7) and Hereditary Spastic Paraplegia (HSP). MFM-7 is an early onset muscle disorder with an autosomal recessive inheritance marked by progressive muscle weakness and joint contractures. Herein, we describe an Iranian family with MFM-7 caused by a homozygous novel variant in KY. We identified a homozygous variant (NM_178554.6:c.1247T > A, p. Ile416Asn) in KY in two patients born to consanguineous parents and the same heterozygous mutation in their parent by Whole-Exome Sequencing. The patients manifest muscle weakness, muscle atrophy, mobility restriction, and hyporeflexia. Lastly, we reviewed the phenotype and corresponding genotype of the previously reported cases with pathogenic variants in KY.

ZNF142 mutation causes neurodevelopmental disorder with speech impairment and seizures: Novel variants and literature review.

The ZNF142 gene on chromosome 2q35 contains ten exons and encodes a zinc finger protein 142 with 31 C2H2-type zinc fingers domain. Pathogenic variants in ZNF142 result in an autosomal recessive neurodevelopmental disorder with impaired speech and developmental delay. Here, we report two novel variants (NM_001105537: c.25C > T/c.1741C > T, p.Gln9*/p.Arg581Cys) in ZNF142 in an Iranian family identified by Whole-Exome sequencing and confirmed by Sanger sequencing. These variants are categorized as "pathogenic" and "variant of unknown significance" based on the standards for the interpretation of sequence variations recommended by ACMG, respectively. The proband is a five-year-old male born to consanguineous parents. The compound heterozygous variant (NM_001105537: c.25C > T/c.1741C > T, p.Gln9*/p.Arg581Cys) in ZNF142 was identified in the proband with moderate intellectual disability, global developmental delay, speech impairment, and seizures. This paper reported the sixth family in the world with novel pathogenic variants in the ZNF142 gene as the reason for neurodevelopmental Disorder with Impaired Speech and Hyperkinetic Movements (NEDISHM) and determining the phenotype spectrum of this disease. In this study, we also reviewed the phenotype of the former cases. In contrast to the Malaysian cases, proband in the present paper does not manifest any facial features similar to the patients in the initial study. Further studies on the NEDISHM patients could be valuable to determine the phenotype precisely.

Phenotypic spectrum of autosomal recessive Keratitis-Ichthyosis-Deafness Syndrome (KIDAR) due to mutations in AP1B1.

Inborn errors in copper metabolism result in a diverse set of abnormalities such as Wilson disease and MEDNIK syndrome. Homozygous pathogenic variants in AP1B1 lead to KIDAR (Keratitis-Ichthyosis-Deafness Syndrome). The main phenotypic features of KIDAR are ichthyosis, keratitis, erythroderma, and progressive hearing loss accompanied by developmental delay and failure to thrive. Herein, we describe a six-and-a-half-year-old boy with KIDAR caused by a novel pathogenic variant in AP1B1 (NM_001127.4:c.1263C > A, p.Tyr421*). The proband presented with ichthyosis, erythroderma, palmoplantar keratoderma, hearing loss, and corneal scarring. He also had hypotonia, global developmental delay, and photophobia. Lastly, we review all of the previously reported cases and the clinical features associated with KIDAR.

Clinical features of patients with Yin Yang 1 deficiency causing Gabriele-de Vries syndrome: A new case and review of the literature.

BACKGROUND: Gabriele-de Vries syndrome is a rare autosomal dominant genetic disease caused by de novo pathogenic variants in YY1. In this study, we report a 10-year-old boy with a de novo novel pathogenic variant in YY1, the first Iranian patient with Gabriele-de Vries Syndrome. METHODS: The novel de novo pathogenic variant detected in this study (NM_003403:c.690delA, p.Glu231Ilefs*25) was identified by whole-exome sequencing and confirmed by Sanger sequencing. RESULTS: The proband presented with delayed motor and speech development, ataxia, abnormal gait, autistic behavior, brain atrophy, and severe learning disability. Finally, we provide a case-based review of the clinical features associated with Gabriele-de Vries Syndrome. Thus far, merely 13 Gabriele-de Vries Syndrome patients have been reported in the literature. CONCLUSION: The investigations for a suspected case of Gabriele-de Vries Syndrome must involve molecular diagnosis of the disease and its underlying genetic defect because the clinical investigations are generally variable and nonspecific.

A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature.

Pathogenic mutations in TDP2, encoding tyrosyl DNA phosphodiesterase 2, cause Spinocerebellar Ataxia autosomal recessive 23 (SCAR23). It is a rare autosomal recessive disorder and mainly has been reported in the European population. Thus far, merely eight patients harboring four TDP2 variants have been reported in the literature. In this study, a novel pathogenic variant (NM_016614: c.4G > T, p.Glu2*) was identified by Whole-Exome and confirmed by Sanger sequencing. The proband has both intellectual and developmental delay, dysphasia, elbow contracture, and upward gaze. The elbow contracture has not been previously described in previous SCAR23 cases. Lastly, we briefly review the phenotypic features of the patients with SCAR23 in the literature.

Two novel Warburg micro syndrome 1 cases caused by pathogenic variants in RAB3GAP1.

In this study, we detected a novel pathogenic variant and a previously reported variant in RAB3GAP1 by whole-exome sequencing (NM_001172435.2: c.1552C>T, p.Gln518*; c.1471C>T, p.Arg491*). The first patient is a 3-year-old girl who presented with bilateral congenital cataracts, developmental delay, abnormal craniofacial features, drug-resistant constipation, and corpus callosum hypoplasia. The proband of the second family is a 13-year-old boy who suffers from developmental delay, quadriplegia, intellectual disability, abnormal craniofacial features, and corpus callosum hypoplasia.

A novel frameshift pathogenic variant in ST3GAL5 causing salt and pepper developmental regression syndrome (SPDRS): A case report.

GM3 synthase deficiency is associated with salt and pepper developmental regression syndrome (SPDRS), a rare genetic disorder. Herein, we report the first Iranian patient with SPDRS. We detected a novel pathogenic variant of ST3GAL5 (NM_003896.4: c.1030_1031del, p.Ile344Cysfs*11). The proband had intellectual disability (ID), failure to thrive, cerebral atrophy, microcephaly, and atonic seizures. The main future challenge proceeding from the results of this study is the prenatal detection of the newly discovered variant; the next step would involve further studies to elucidate the phenotypic spectrum of SPDRS and detect new variants that could cause symptoms ranging from mild to severe.

A novel PTRH2 missense mutation causing IMNEPD: a case report.

PTRH2 deficiency is associated with an extremely rare disease, infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD). We report the first Iranian patient with IMNEPD. We detected a pathogenic variant in the PTRH2 gene (NM_016077.5: c.68T > C, p.V23A). The proband has myopia, spastic diplegic cerebral palsy, urolithiasis, and a history of seizures.

Phenotype of ST3GAL3 deficient patients: A case and review of the literature.

ST3GAL3 deficiency is an extremely rare autosomal recessive disorder caused by pathogenic mutations in the ST3GAL3 gene. Epilepsy, motor development delay, severe intellectual disability, and behavioral disorders have been reported to be associated with ST3GAL3 deficiency. In the present study, ST3GAL3 deficiency was caused by a homozygous splice-site mutation (NM_174964.4: c.936+1delG) in ST3GAL3. The patient described in this study was clinically similar to previously reported cases; nevertheless, we were able to detect repetitive behavior, previously not reported manifestations.