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Human Genome Variation

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https://www.readbyqxmd.com/read/29899997/two-novel-mutations-of-comp-in-japanese-boys-with-pseudoachondroplasia
#1
Yosuke Ichihashi, Masaki Takagi, Tomohiro Ishii, Kenji Watanabe, Gen Nishimura, Tomonobu Hasegawa
Mutations in the cartilage oligomeric matrix protein ( COMP ) gene cause both pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED). Most mutations in COMP are located in the region encoding type 3 thrombospondin like domain (TSP3D). We report two Japanese boys with PSACH who had different novel in-frame deletions in TSP3D. The result recapitulates previous reports in that the in-frame deletions in TSP3D preferentially caused PSACH rather than MED.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29899996/biallelic-mutations-of-egfr-in-a-compound-heterozygous-state-cause-ectodermal-dysplasia-with-severe-skin-defects-and-gastrointestinal-dysfunction
#2
Shion Hayashi, Takayuki Yokoi, Chihiro Hatano, Yumi Enomoto, Yoshinori Tsurusaki, Takuya Naruto, Masahisa Kobayashi, Hiroyuki Ida, Kenji Kurosawa
Epidermal growth factor receptor (EGFR), a receptor that recognizes epidermal growth factor, is a very important regulator of cell proliferation and differentiation. To date, three cases of severe ectodermal dysplasia were reported to be caused by an inherited germline homozygous loss-of-function missense mutation of EGFR . This is the first report of a patient with biallelic compound heterozygous mutations in EGFR .
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29899995/high-resolution-melting-analysis-coupled-with-next-generation-sequencing-as-a-simple-tool-for-the-identification-of-a-novel-somatic-brca2-variant-a-case-report
#3
Alessandra Costella, Rossella De Leo, Donatella Guarino, Marco D'Indinosante, Paola Concolino, Giorgia Mazzuccato, Andrea Urbani, Giovanni Scambia, Ettore Capoluongo, Anna Fagotti, Angelo Minucci
In a 72-year-old woman with no associated personal or family history of breast and/or ovarian cancers, we identified a novel somatic pathogenic BRCA2 variant ( c.18_28delAGAGAGGCCAA , p.Lys6Asnfs*4) using next-generation sequencing (NGS). The variant allele frequency (VAF) was 16%, and Sanger sequencing was unable to identify this variant. Adopting a high-resolution melting analysis strategy coupled with NGS, we successfully highlighted the presence of the c.18_28delAGAGAGGCCAA allele.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29899994/two-novel-vcp-missense-variants-identified-in-japanese-patients-with-multisystem-proteinopathy
#4
Michio Inoue, Aritoshi Iida, Shinichiro Hayashi, Madoka Mori-Yoshimura, Atsushi Nagaoka, Shunsuke Yoshimura, Hirokazu Shiraishi, Akira Tsujino, Yuji Takahashi, Ikuya Nonaka, Yukiko K Hayashi, Satoru Noguchi, Ichizo Nishino
VCP mutations were first associated with inclusion body myopathy with Paget's disease of bone and frontotemporal dementia (IBMPFD) but was later associated with amyotrophic lateral sclerosis and Charcot-Marie-Tooth disease. Now, a new name, "multisystem proteinopathy (MSP)", is proposed for this condition. VCP encodes valosin-containing protein, which is involved in protein degradation in the ubiquitin proteasome system. We report here two MSP patients with two novel heterozygous missense variants in VCP : c...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29899993/genitopatellar-syndrome-the-first-reported-case-in-japan
#5
Satomi Okano, Akie Miyamoto, Ikue Fukuda, Hajime Tanaka, Kenichiro Hata, Tadashi Kaname, Yoichi Matsubara, Yoshio Makita
Genitopatellar syndrome (GPS) is mainly characterized by an absence of patellae, congenital flexion contractures of the lower limbs, psychomotor retardation, and anomalies of the external genitalia and kidneys. We report an 18-year-old female with a novel heterozygous truncating mutation in exon 17 of the KAT6B gene [MC_000010.11:c.3603_3606 del, p.Arg1201fs]. This is the first report of typical GPS in a Japanese individual. The details of our findings may contribute to elucidating the mechanism underlying GPS-specific clinical features...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29844917/identification-of-a-rare-bmp-pathway-mutation-in-a-non-syndromic-human-brain-arteriovenous-malformation-via-exome-sequencing
#6
Brian P Walcott, Ethan A Winkler, Sirui Zhou, Harjus Birk, Diana Guo, Matthew J Koch, Christopher J Stapleton, Dan Spiegelman, Alexandre Dionne-Laporte, Patrick A Dion, Kristopher T Kahle, Guy A Rouleau, Michael T Lawton
Brain arteriovenous malformations (AVMs) are abnormal connections between arteries and veins that can result in hemorrhagic stroke. A genetic basis for AVMs is suspected, and we investigated potential mutations in a 14-year-old girl who developed a recurrent brain AVM. Whole-exome sequencing (WES) of AVM lesion tissue and blood was performed accompanied by in silico modeling, protein expression observation in lesion tissue and zebrafish modeling. A stop-gain mutation (c.C739T:p.R247X) in the gene SMAD family member 9 ( SMAD9 ) was discovered...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29796286/a-novel-8-bp-duplication-in-adat3-causes-mild-intellectual-disability
#7
Ahmad Reza Salehi Chaleshtori, Noriko Miyake, Mohammad Ahmadvand, Oranous Bashti, Naomichi Matsumoto, Mehrdad Noruzinia
Inosine is a base located at wobble position 34 of the tRNA anticodon stem-loop, enabling the recognition of more than one codon in the translation process. A heterodimer consists of ADAT3 and ADAT2 and is involved in the adenosine-to-inosine conversion in tRNA. Here, we report the second novel ADAT3 mutation in a patient with microcephaly, intellectual disability, and hyperactivity. These findings constitute a second mutation and expand the clinical spectrum of extremely rare ADAT3 mutations.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29796285/myelodysplastic-syndrome-in-an-infant-with-constitutional-pure-duplication-1q41-qter
#8
Hirokazu Morokawa, Motoko Kamiya, Keiko Wakui, Mikiko Kobayashi, Takashi Kurata, Kazuyuki Matsuda, Rie Kawamura, Hiroyuki Kanno, Yoshimitsu Fukushima, Yozo Nakazawa, Tomoki Kosho
We report on a Japanese female infant as the fourth patient with the constitutional pure duplication 1q41-qter confirmed by chromosomal microarray and as the first who developed myelodysplastic syndrome (MDS) among those with the constitutional 1q duplication. Common clinical features of the constitutional pure duplication 1q41-qter include developmental delay, craniofacial characteristics, foot malformation, hypertrichosis, and respiratory insufficiency. The association between MDS and the duplication of the genes in the 1q41-qter region remains unknown...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29760939/novel-tfap2a-mutation-in-a-japanese-family-with-branchio-oculo-facial-syndrome
#9
Taisuke Sato, Osamu Samura, Noriko Kato, Kosuke Taniguchi, Ken Takahashi, Yuki Ito, Hiroaki Aoki, Masahisa Kobayashi, Ohsuke Migita, Aikou Okamoto, Kenichiro Hata
Branchio-oculo-facial syndrome (BOFS) is a rare autosomal dominant disorder characterized by craniofacial, ocular, and ectodermal anomalies. BOFS is caused by mutation of the transcription factor AP2-alpha gene ( TFAP2A ). We performed detailed genetic analysis of a Japanese family with clinically suspected BOFS and identified a novel missense mutation resulting in a predicted amino-acid substitution in the highly conserved basic DNA-binding domain of TFAP2A (NM_003220.2:c.699A>C).
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29760938/novel-col4a1-mutation-in-a-fetus-with-early-prenatal-onset-of-schizencephaly
#10
Yota Sato, Jun Shibasaki, Noriko Aida, Kazuya Hiiragi, Yuichi Kimura, Moe Akahira-Azuma, Yumi Enomoto, Yoshinori Tsurusaki, Kenji Kurosawa
Porencephaly and schizencephaly are congenital brain disorders that can be caused by COL4A1 mutations, though the underlying mechanism and developmental processes are poorly understood. Here, we report a patient with schizencephaly, detected by fetal ultrasonography and fetal magnetic resonance imaging, with a de novo novel mutation in COL4A1 (c.2645_2646delinsAA, p.Gly882Glu). Our results suggest that the onset of damage that potentially results in schizencephaly occurs mid-pregnancy.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29760937/a-novel-mlh1-intronic-variant-in-a-young-japanese-patient-with-lynch-syndrome
#11
Yoshimi Kiyozumi, Hiroyuki Matsubayashi, Yasue Horiuchi, Takuma Oishi, Masato Abe, Sumiko Ohnami, Akane Naruoka, Masatoshi Kusuhara, Ken Yamaguchi
Lynch syndrome, an autosomal dominantly inherited disease, is characterized by an increased risk of developing colorectal cancer. We found a novel germline variant of MLH1 (IVS6+2T>C) that caused Lynch syndrome in a young Japanese patient who had multiple colorectal cancers. Accurate diagnosis will be highly beneficial in clinical practice for surveillance and genetic counseling of patients and their relatives.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29760936/preliminary-molecular-evidence-associating-a-novel-brca1-synonymous-variant-with-hereditary-ovarian-cancer-syndrome
#12
Angelo Minucci, Paola Concolino, Maria De Bonis, Alessandra Costella, Ida Paris, Giovanni Scambia, Ettore Capoluongo
Extensive molecular screening of the BRCA1/2 ( BRCA) genes by massively parallel sequencing (MPS) identified variants of uncertain (or unknown) significance (VUS) and novel variants. We performed a molecular characterization of a novel BRCA1 synonymous variant discovered in a family with hereditary ovarian cancer (HOC) syndrome. We showed that the BRCA1 c.5073   A  > T variant might play a pathogenic role in HOC syndrome in this family.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29736252/a-novel-s269c-mutation-in-fibroblast-growth-factor-receptor-3-in-a-japanese-child-with-hypochondroplasia
#13
Ikuko Takahashi, Daiki Kondo, Chikako Oyama, Tamami Yano, Hiroaki Tamura, Atsuko Noguchi, Tsutomu Takahashi
Functionally activating mutations in fibroblast growth factor receptor 3 (FGFR3) can cause four types of autosomal dominant skeletal dysplasia with short-limbed dwarfism that include the mildest phenotype, hypochondroplasia (HCH). A novel mutation (c.805A>T, p.S269C) was identified in a Japanese infant with HCH through direct sequencing of all FGFR3 exons and exon/intron boundaries. This mutation creates an additional cysteine residue in the extracellular region of FGFR3 that results in the functional activation of FGFR3...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29644085/protein-molecular-modeling-shows-residue-t599-is-critical-to-wild-type-function-of-polg-and-description-of-a-novel-variant-associated-with-the-sando-phenotype
#14
John E Richter, Hector G Robles, Elizabeth Mauricio, Ahmed Mohammad, Paldeep S Atwal, Thomas R Caulfield
Sensory ataxic neuropathy with dysarthria and ophthalmoparesis (SANDO) is a rare phenotype resulting from pathogenic variants of mitochondrial DNA polymerase gamma ( POLG ). We modeled a novel POLG variant, T599P, that causes the SANDO phenotype and another variant at the same residue, p.T599E, to observe their effect on protein function and confirm the pathogenicity of T599P. Through neoteric molecular modeling techniques, we show that changes at the T599 residue position introduce extra rigidity into the surrounding helix-loop-helix, which places steric pressure on nearby nucleotides...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29644084/primary-microcephaly-caused-by-novel-compound-heterozygous-mutations-in-aspm
#15
Nobuhiko Okamoto, Tomohiro Kohmoto, Takuya Naruto, Kiyoshi Masuda, Issei Imoto
Autosomal recessive primary microcephaly (microcephaly primary hereditary, MCPH) is a genetically heterogeneous rare developmental disorder that is characterized by prenatal onset of abnormal brain growth, which leads to intellectual disability of variable severity. We report a 5-year-old male who presented with a severe form of primary microcephaly. Targeted panel sequencing revealed compound heterozygous truncating mutations of the abnormal spindle-like microcephaly-associated ( ASPM ) gene, which confirmed the MCPH5 diagnosis...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29619239/novel-compound-heterozygous-variants-in-the-larp7-gene-in-a-patient-with-alazami-syndrome
#16
Sumito Dateki, Tasuku Kitajima, Toshiharu Kihara, Satoshi Watanabe, Koh-Ichiro Yoshiura, Hiroyuki Moriuchi
The LARP7 gene encodes a chaperone protein of the noncoding RNA 75 K, and mutations in this gene have been identified in patients with Alazami syndrome. Herein, we report another Japanese patient with Alazami syndrome and novel compound heterozygous variants in LARP7 (i.e., c.370delG, p.Glu124fs*38 and c.641_667+25del involving the splice donor site of intron 8). These findings provide further evidence that biallelic LARP7 defects cause the phenotype of Alazami syndrome.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29619238/pelizaeus-merzbacher-disease-can-be-a-differential-diagnosis-in-males-presenting-with-severe-neonatal-respiratory-distress-and-hypotonia
#17
Ayako Ueda, Hiroko Shimbo, Yukari Yada, Yasunori Koike, Takanori Yamagata, Hitoshi Osaka
Pelizaeus-Merzbacher disease (PMD; MIM #312080) is a rare X-linked recessive disorder. A male neonate presented with severe respiratory distress that required tracheostomy. After the appearance of nystagmus, PMD was suspected as a diagnosis for the patient, and a missense mutation, p.Phe51Val, was identified in PLP1 , the gene responsible for PMD. PMD can be a differential diagnosis in a male neonate presenting severe respiratory distress.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29619237/refining-the-clinical-phenotype-of-okur-chung-neurodevelopmental-syndrome
#18
Moe Akahira-Azuma, Yoshinori Tsurusaki, Yumi Enomoto, Jun Mitsui, Kenji Kurosawa
We describe an 8-year-old Japanese boy with a de novo recurrent missense mutation in CSNK2A1 , c.593A>G, that is causative of Okur-Chung neurodevelopmental syndrome. He exhibited distinctive facial features, severe growth retardation with relative macrocephaly, and friendly, hyperactive behavior. His dysmorphic features might suggest a congenital histone modification defect syndrome, such as Kleefstra, Coffin-Siris, or Rubinstein-Taybi syndromes, which are indicative of functional interactions between the casein kinase II, alpha 1 gene and histone modification factors...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29619236/evaluation-of-the-isl1-gene-in-the-pathogenesis-of-bladder-exstrophy-in-a-swedish-cohort
#19
Samara Arkani, Jia Cao, Johanna Lundin, Daniel Nilsson, Thomas Källman, Gillian Barker, Gundela Holmdahl, Christina Clementsson Kockum, Hans Matsson, Agneta Nordenskjöld
Bladder exstrophy is a congenital closure defect of the urinary bladder with a profound effect on morbidity. Although the malformation is usually sporadic, a genetic background is supported by an increased recurrence risk in relatives, higher concordance rates in monozygotic twins and several associated chromosomal aberrations. Recently, the ISL1 gene was presented as a candidate gene for bladder exstrophy and epispadias complex (BEEC) development in two different studies. In our study, we screened for genetic variants in the ISL1 gene in DNA from 125 Swedish patients using Sanger sequencing and array-CGH analysis...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29619235/imethyl-an-integrative-database-of-human-dna-methylation-gene-expression-and-genomic-variation
#20
Shohei Komaki, Yuh Shiwa, Ryohei Furukawa, Tsuyoshi Hachiya, Hideki Ohmomo, Ryo Otomo, Mamoru Satoh, Jiro Hitomi, Kenji Sobue, Makoto Sasaki, Atsushi Shimizu
We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database...
2018: Human Genome Variation
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