• Genes and Genomics
• /
• 제40권11호
• /
• pp.1149-1155
• /
• 2018

Epileptic encephalopathies are genetically heterogeneous disorders which leads to epilepsy and cause neurological disorders. Seizure threshold 2 (SZT2) gene located on chromosome 1p34.2 encodes protein mainly expressed predominantly in the parietal and frontal cortex and dorsal root ganglia in the brain. Previous studies in mice showed that mutation in this gene can confers low seizure threshold, enhance epileptogenesis and in human may leads to facial dysmorphism, intellectual disability, seizure and macrocephaly. Objective of this study was to find out novel gene or novel mutation related to the gene phenotype. We have identified a large consanguineous Saudi family segregating developmental delay, intellectual disability, epilepsy, high forehead and macrocephaly. Exome sequencing was performed in affected siblings of the family to study the novel mutation. Whole exome sequencing data analysis, confirmed by subsequent Sanger sequencing validation study. Our results showed a novel homozygous mutation (c.9368G>A) in a substitution of a conserved glycine residue into a glutamic acid in the exon 67 of SZT2 gene. The mutation was ruled out in 100 unrelated healthy controls. The missense variant has not yet been reported as pathogenic in literature or variant databases. In conclusion, the here detected homozygous SZT2 variant might be the causative mutation that further explain epilepsy and developmental delay in this Saudi family.

• Journal of Genetic Medicine
• /
• 제15권2호
• /
• pp.102-106
• /
• 2018

Aggrecan is a proteoglycan in the extracellular matrix of growth plate and cartilaginous tissues. Aggrecanopathy has been reported as a genetic cause not only for severe skeletal dysplasia but also for autosomal dominant short stature with normal to advanced bone age. We report a novel heterozygous mutation of ACAN in a Korean family with proportionate short stature identified through targeted exome sequencing. We present a girl of 4 years and 9 months with a family history of short stature over three generations. The paternal grandmother is 143 cm tall (-3.8 as a Korean standard deviation score [SDS]), the father 155 cm (-3.4 SDS), and the index case 96.2 cm (-2.9 SDS). Evaluation for short stature showed normal growth hormone (GH) peaks in the GH provocation test and a mild delayed bone age for chronological age. This subject had clinical characteristics including a triangular face, flat nasal bridge, prognathia, blue sclerae, and brittle teeth. The targeted exome sequencing was applied to detect autosomal dominant growth palate disorder. The novel variant c.910G>A (p.Asp304Asn) in ACAN was identified and this variant was found in the subject's father using Sanger sequencing. This is the first case of Korean familial short stature due to ACAN mutation. ACAN should be considered for proportionate idiopathic short stature, especially in cases of familial short stature.

• Journal of Yeungnam Medical Science
• /
• 제38권2호
• /
• pp.160-164
• /
• 2021

Oculocutaneous albinism (OCA) is a group of rare genetically heterogeneous disorders, characterized by hypopigmentation of the eyes, skin, and hair, which result in ocular abnormalities and a risk of developing skin cancer. Currently, there is no ophthalmologic procedure or drug that prevents the clinical features of OCA. Here, we report a new type of OCA in two, unrelated Korean families with the same OCA2 mutation. Affected individuals in this study are different from those of previous reports in two aspects: an inheritance pattern and clinical presentation. All reported patients with OCA have shown an autosomal recessive inheritance pattern, while our patients showed an autosomal dominant inheritance pattern. Small amounts of pigment can be acquired with age in OCA, but there is no substantial variation from adolescence to adulthood in this regard. A case where the patient attained normal pigmentation levels has never been reported. However, our patients displayed completely normal pigmentation in their late twenties. Whole exome sequencing and in-silico analysis revealed a novel mutation, OCA2 c.2338G>A p.(G780S) (NM_000275) with a high likelihood of pathogenicity. Sanger sequencing of p.G780S identified the same mutation in the affected individuals, which was not found in the family members with normal phenotype. We hypothesize that OCA2 G780S not only acts as a pathogenic variant of OCA but also induces pigmentation by enhancing the melanogenesis gene expression of other modifier genes, such as SLC45A2 and TPC2. These findings may provide further understanding of melanin biosynthesis and new treatment methods for OCA.

• Genomics & Informatics
• /
• 제15권4호
• /
• pp.136-141
• /
• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• 대한유전성대사질환학회지
• /
• 제17권2호
• /
• pp.69-76
• /
• 2017

Citrin 결핍증은 요소회로 이상 질환 중 하나로, 7q21.3에 위치한 SLC25A13 유전자에 돌연변이로 발생하는 상염색체 열성 유전질환이다. 세 가지 표현형 중에 신생아 간내 담즙 정체형, 제 2형 시트룰린혈증은 잘 알려졌지만, 성장부진과 이상지질혈증형은 최근에 밝혀지고 있는 표현형으로 아직 우리나라에 보고된 적이 없다. 성장부진과 이상지질혈증형에서는 경미할 수는 있으나 식욕감소, 피곤함, 성장부진, 저혈당, 시트룰린 상승, 이상지질혈증, 젖산염/피루브산염 상승과 같은 이상이 관찰될 수 있다. 또한 저혈당으로 내원하였을 때 일반적인 검사로는 원인 규명이 어려울 수 있다. 저자들은 생후 30개월에 반복적인 저혈당으로 내원하여 소변 유기산 분석, 호르몬 검사와 같은 대사 이상 검사에서 명확한 특정 진단명이 의심되지 않아, 생후 31개월에 targeted exome sequencing을 통해 복합이형접합 SLC25A13 유전자 돌연변이[c.852_855del (p.Met285Profs*2), c.1177+1G>A]를 발견하여 성장부진과 이상지질혈증으로 발현한 citrin 결핍증을 우리나라에서 최초로 진단하여 보고하는 바이다.

• 생명과학회지
• /
• 제24권3호
• /
• pp.311-317
• /
• 2014

Rimed vacuole을 가진 원위 근육병(distal myopathy with rimmed vacuoles, DMRV)은 제2형 유전성 봉입체 근육병으로도 불리며 초기 성인기에 발병하여 원위부의 근력약화를 보이는 임상양상과 rimmed vacuole의 근육병리소견을 특징으로 하는 상염색체 열성의 근육병이다. 이러한 DMRV의 원인은 UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) 유전자의 돌연변이임이 밝혀져 있다. 저자들은 원위부 근력약화를 호소하는 환자에서 전체 엑솜 염기서열분석을 이용하여 GNE 유전자의 복합 이형접합성 돌연변이(p.Asp176Val 및 p.Val572Leu)를 확인하여 DMRV를 진단할 수 있었다. 본 연구는 근육병의 정확한 분자진단에 있어서 전체 엑솜 염기서열분석의 유용성을 보여주었기에 이를 보고하는 바이다.

• Genomics & Informatics
• /
• 제20권2호
• /
• pp.24.1-24.8
• /
• 2022

Hypomyelinating leukodystrophy type 2 (HLD2), is an inherited genetic disease of the central nervous system caused by recessive mutations in the gap junction protein gamma 2 (GJC2/GJA12). HLD2 is characterized by nystagmus, developmental delay, motor impairments, ataxia, severe speech problem, and hypomyelination in the brain. The GJC2 sequence encodes connexin 47 protein (Cx47). Connexins are a group of membrane proteins that oligomerize to construct gap junctions protein. In the present study, a novel missense mutation gene c.760G>A (p.Val254Met) was identified in a patient with HLD2 by performing whole exome sequencing. Following the discovery of the new mutation in the proband, we used Sanger sequencing to analyze his affected sibling and parents. Sanger sequencing verified homozygosity of the mutation in the proband and his affected sibling. The autosomal recessive inheritance pattern was confirmed since Sanger sequencing revealed both healthy parents were heterozygous for the mutation. PolyPhen2, SIFT, PROVEAN, and CADD were used to evaluate the function prediction scores of detected mutations. Cx47 is essential for oligodendrocyte function, including adequate myelination and myelin maintenance in humans. Novel mutation p.Val254Met is located in the second extracellular domain of Cx47, both extracellular loops are highly conserved and probably induce intramolecular disulfide interactions. This novel mutation in the Cx47 gene causes oligodendrocyte dysfunction and HLD2 disorder.

• Journal of Genetic Medicine
• /
• 제16권1호
• /
• pp.27-30
• /
• 2019

Smith-Kingsmore syndrome (SKS; OMIM 616638), also known as macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (MINDS; ORPHA 457485), is a rare autosomal dominant disorder, the prevalence of which is not known. It is caused by a heterozygous germline mutation in MTOR (OMIM 601231). Ten different MTOR germline mutations in 27 individuals have been reported in the medical literature to date. These were all gain-of-function missense variants, and about half of the 27 individuals had c.5395G>A p.(Glu1799Lys) in MTOR. Here, I report for the first time a Korean patient with the heterozygous germline mutation c.5395G>A p.(Glu1799Lys) in MTOR. It was found to be a de novo mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing. The patient showed typical clinical features of SKS, including macrocephaly/megalencephaly; moderate intellectual disability; seizures; behavioral problems; and facial dysmorphic features of curly hair, frontal bossing, midface hypoplasia, and hypertelorism.

• Journal of Genetic Medicine
• /
• 제18권1호
• /
• pp.70-74
• /
• 2021

Cohen-Gibson syndrome (CGS) was first reported by Cohen et al., who identified the mutation of the gene encoding the embryonic ectoderm development (EED) in a patient with phenotypes similar to Weaver syndrome. CGS manifests as an overgrowth and intellectual disability, in addition to the characteristic facial features and organ anomalies. CGS has been reported in only 11 unrelated patients since 2015. A girl aged 6 years and 3 months presented with seizures. She had macrosomia, a dysmorphic face, and intellectual disability. Her mother and younger sister and brother also had macrosomia, intellectual disability, and similar facial features; additionally, her mother experienced seizures and had an arachnoid cyst, while her siblings had valvar pulmonary stenosis. Whole-exome sequencing for the proband revealed a mutation of EED (c.581A>G, p.Asn194Ser), which was also verified in the mother and both siblings using Sanger sequencing. This is the first report of familial CGS.

• Genomics & Informatics
• /
• 제13권4호
• /
• pp.126-131
• /
• 2015

Fulminant type 1 diabetes (T1DM) is a distinct subtype of T1DM that is characterized by rapid onset hyperglycemia, ketoacidosis, absolute insulin deficiency, and near normal levels of glycated hemoglobin at initial presentation. Although it has been reported that class II human leukocyte antigen (HLA) genotype is associated with fulminant T1DM, the genetic predisposition is not fully understood. In this study we investigated the HLA genotype and haplotype in 11 Korean cases of fulminant T1DM using imputation of whole exome sequencing data and compared its frequencies with 413 participants of the Korean Reference Panel. The $HLA-DRB1^*04:05-HLA-DQB1^*04:01$ haplotype was significantly associated with increased risk of fulminant T1DM in Fisher's exact test (odds ratio [OR], 4.11; 95% confidence interval [CI], 1.56 to 10.86; p = 0.009). A histidine residue at $HLA-DR{\beta}1$ position 13 was marginally associated with increased risk of fulminant T1DM (OR, 2.45; 95% CI, 1.01 to 5.94; p = 0.054). Although we had limited statistical power, we provide evidence that HLA haplotype and amino acid change can be a genetic risk factor of fulminant T1DM in Koreans. Further large-scale research is required to confirm these findings.