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Human Genome Variation

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https://read.qxmd.com/read/30886724/a-novel-compound-heterozygous-mutation-in-ttc8-identified-in-a-japanese-patient
#1
Shigeru Sato, Takeshi Morimoto, Kikuko Hotta, Takashi Fujikado, Kohji Nishida
Bardet-Biedl syndrome (BBS), characterized by rod-cone dystrophy, postaxial polydactyly, central obesity, hypogonadism, renal abnormalities, and mental retardation, is a rare autosomal recessive disorder. To date, 21 causative genes have been reported. Here we describe a Japanese BBS patient with a novel compound heterozygous mutation in TTC8 . To the best of our knowledge, this is the first description of a BBS patient with a mutation in the TTC8 gene in Japan.
2019: Human Genome Variation
https://read.qxmd.com/read/30854216/a-novel-germline-mutation-of-the-sftpa1-gene-in-familial-interstitial-pneumonia
#2
Martina Doubková, Kateřina Staňo Kozubík, Lenka Radová, Michaela Pešová, Jakub Trizuljak, Karol Pál, Klára Svobodová, Kamila Réblová, Hana Svozilová, Zuzana Vrzalová, Šárka Pospíšilová, Michael Doubek
Different genes related to alveolar stability have been associated with familial interstitial pneumonia (FIP). Here, we report a novel, rare SFTPA1 variant in a family with idiopathic interstitial pneumonia (IIP). We performed whole-exome sequencing on germline DNA samples from four members of one family; three of them showed signs of pulmonary fibrosis (idiopathic interstitial pneumonia) with autosomal-dominant inheritance. A heterozygous single nucleotide variant c.532 G > A in the SFTPA1 gene has been identified...
2019: Human Genome Variation
https://read.qxmd.com/read/30820325/a-novel-variant-in-fn1-in-a-family-with-fibronectin-glomerulopathy
#3
Nabeel Aslam, Anshika Singh, Cherise Cortese, Douglas L Riegert-Johnson
Glomerulopathy with fibronectin deposits (GFND) is a rare glomerular disorder. We report a 28-year-old male diagnosed with GFND by mass spectrometry on kidney biopsy tissue. Whole-exome sequencing (WES) identified that a previously undescribed FN1 gene mutation (c.3051G > T, p.W1017C) was likely responsible for this patient's fibronectin glomerulopathy. We discuss the implications of this novel variant of FN1 and the importance of WES to identify a mutation in a gene of interest.
2019: Human Genome Variation
https://read.qxmd.com/read/30820324/a-healthy-individual-with-a-homozygous-ptch2-frameshift-variant-are-variants-of-ptch2-associated-with-nevoid-basal-cell-carcinoma-syndrome
#4
M Altaraihi, K Wadt, J Ek, A M Gerdes, E Ostergaard
Variants in PTCH2 have been described to be associated with Nevoid Basal Cell Carcinoma Syndrome (NBCCS). We report a family with a healthy female who is homozygous for a frameshift variant, c.269delG, p.(Gly90Alafs*4), in PTCH2 and her heterozygous daughter. The variant predicts a frameshift and a premature stop codon. A summary of reported heterozygous individuals with germline PTCH2 variants along with the existence of a healthy homozygous individual question whether variants in PTCH2 are associated with NBCCS...
2019: Human Genome Variation
https://read.qxmd.com/read/30792871/a-novel-phex-mutation-associated-with-vitamin-d-resistant-rickets
#5
Saori Sako, Yo Niida, Kosuke Robert Shima, Yumie Takeshita, Kiyo-Aki Ishii, Toshinari Takamura
X-linked hypophosphatemic rickets (XLH) is the most common form of hereditary rickets. Here, we present a case of XLH associated with a novel mutation in a phosphate-regulating gene with homologies to endopeptidases on the X chromosome ( PHEX ). PCR-direct sequencing revealed a novel PHEX mutation in exon 22, NM_000444.6( PHEX ):c.2202del [p.Asn736Ilefs*4], near the 3'-UTR region encoding the COOH-terminal extracellular domain. In silico analysis indicated that a single mutation in N736 may have caused a significant change in higher-order protein structure and function...
2019: Human Genome Variation
https://read.qxmd.com/read/30774966/novel-compound-heterozygous-cdh23-variants-in-a-patient-with-usher-syndrome-type-i
#6
Satomi Okano, Yoshio Makita, Akihiro Katada, Yasuaki Harabuchi, Tomohiro Kohmoto, Takuya Naruto, Kiyoshi Masuda, Issei Imoto
Usher syndrome type I (USH1) is characterized by congenital, bilateral, profound sensorineural hearing loss, vestibular areflexia, and adolescent-onset retinitis pigmentosa. Here, we report a 12-year-old female patient with typical USH1. Targeted panel sequencing revealed compound heterozygous variants of the Cadherin 23 ( CDH23 ) gene, which confirmed the USH1 diagnosis. A novel NM_022124.5:c.130G>A/p.(Glu44Lys) was identified, expanding the mutation spectrum of CDH23 .
2019: Human Genome Variation
https://read.qxmd.com/read/30701076/activation-of-tgf-%C3%AE-signaling-in-an-aortic-aneurysm-in-a-patient-with-loeys-dietz-syndrome-caused-by-a-novel-loss-of-function-variant-of-tgfbr1
#7
Hironori Hara, Norifumi Takeda, Takayuki Fujiwara, Hiroki Yagi, Sonoko Maemura, Tsubasa Kanaya, Kan Nawata, Hiroyuki Morita, Issei Komuro
Loeys-Dietz syndrome (LDS) is caused by variants of transforming growth factor-β (TGF-β)-related genes and is characterized by aortic aneurysm and dissection. We report an LDS patient with a de novo missense variant of TGFBR1 [c.1126A>G, p.(Lys376Glu)] in which active TGF-β signaling was observed in the aorta, despite the in vitro demonstration that the loss-of-function mutation lies within the serine/threonine kinase domain. The mechanism underlying this TGF-β paradox in LDS aortopathy should be further investigated...
2019: Human Genome Variation
https://read.qxmd.com/read/30675365/-epi-genetic-defects-of-mkrn3-are-rare-in-asian-patients-with-central-precocious-puberty
#8
Erina Suzuki, Hirohito Shima, Masayo Kagami, Shun Soneda, Toshiaki Tanaka, Shuichi Yatsuga, Junko Nishioka, Yuji Oto, Toshiya Kamiya, Yasuhiro Naiki, Tsutomu Ogata, Yasuko Fujisawa, Akie Nakamura, Sayaka Kawashima, Shuntaro Morikawa, Reiko Horikawa, Shinichiro Sano, Maki Fukami
We sequenced MKRN3 , the major causative gene of central precocious puberty in Western countries, in 24 Japanese or Chinese patients and examined the DNA methylation and copy-number statuses of this gene in 19 patients. We identified no (epi)genetic defects except for one previously reported mutation. These results, together with reports from Korea, indicate that MKRN3 defects are rare in Asian populations. The ethnic differences likely reflect Western country-specific founder mutations and the rarity of de novo mutations...
2019: Human Genome Variation
https://read.qxmd.com/read/30652007/a-new-case-of-spastic-paraplegia-type-64-due-to-a-missense-mutation-in-the-entpd1-gene
#9
Jean Mamelona, Nicolas Crapoulet, Alier Marrero
Spastic paraplegia type 64 (SPG64; OMIM 615683) is a complicated form of hereditary spastic paraplegia (HSP) recently identified in individuals diagnosed with suspected neurodegenerative disease. Affected patients carry homozygous mutations in the ectonucleoside triphosphate diphosphohydrolase 1 gene ( ENTPD1 ). Although they share common characteristics, affected individuals show slight discrepancies in some clinical aspects. At present, only two different cases of SPG64 have been diagnosed. More findings of genetic variation would be helpful to better understand the effect of mutations in the ENTPD1 gene on the neurological condition of affected individuals...
2019: Human Genome Variation
https://read.qxmd.com/read/30652006/genetics-of-narcolepsy
#10
REVIEW
Taku Miyagawa, Katsushi Tokunaga
Narcolepsy is a term that was initially coined by Gélineáu in 1880 and is a chronic neurological sleep disorder that manifests as a difficulty in maintaining wakefulness and sleep for long periods. Currently, narcolepsy is subdivided into two types according to the International Classification of Sleep Disorders, 3rd edition: narcolepsy type 1 (NT1) and narcolepsy type 2 (NT2). NT1 is characterized by excessive daytime sleepiness, cataplexy, hypnagogic hallucinations, and sleep paralysis and is caused by a marked reduction in neurons in the hypothalamus that produce orexin (hypocretin), which is a wakefulness-associated neuropeptide...
2019: Human Genome Variation
https://read.qxmd.com/read/30652005/novel-mutations-in-the-rs1-gene-in-japanese-patients-with-x-linked-congenital-retinoschisis
#11
Hiroyuki Kondo, Kazuma Oku, Satoshi Katagiri, Takaaki Hayashi, Tadashi Nakano, Akiko Iwata, Kazuki Kuniyoshi, Shunji Kusaka, Atsushi Hiyoshi, Eiichi Uchio, Mineo Kondo, Noriko Oishi, Shuhei Kameya, Atsushi Mizota, Nobuhisa Naoi, Shinji Ueno, Hiroko Terasaki, Takeshi Morimoto, Masayoshi Iwaki, Kazutoshi Yoshitake, Daisuke Iejima, Kaoru Fujinami, Kazushige Tsunoda, Kei Shinoda, Takeshi Iwata
X-linked congenital retinoschisis (XLRS) is an inherited retinal disorder characterized by reduced central vision and schisis of the macula and peripheral retina. XLRS is caused by mutations in the RS1 gene. We have identified 37 different mutations in the RS1 gene, including 12 novel mutations, in 67 Japanese patients from 56 XLRS families. We present clinical features of these patients in relation to the associated mutations.
2019: Human Genome Variation
https://read.qxmd.com/read/30622725/novel-neuroblastoma-amplified-sequence-nbas-mutations-in-a-japanese-boy-with-fever-triggered-recurrent-acute-liver-failure
#12
Sahoko Ono, Junko Matsuda, Etsuko Watanabe, Hiroto Akaike, Hideto Teranishi, Ippei Miyata, Takanobu Otomo, Yoshito Sadahira, Tatsuki Mizuochi, Hironori Kusano, Masayoshi Kage, Hiroo Ueno, Kenichi Yoshida, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Seishi Ogawa, Yasuhide Hayashi, Hirokazu Kanegane, Kazunobu Ouchi
Biallelic mutations in the neuroblastoma amplified sequence ( NBAS ) gene have been reported to cause two different clinical spectra: short stature with optic nerve atrophy and Pelger-Huët anomaly (SOPH) syndrome and infantile liver failure syndrome 2 (ILFS2). Here, we describe a case of a 3-year-old Japanese boy who presented with fever-triggered recurrent acute liver failure (ALF). The clinical characteristics were considerable elevation of liver enzymes, severe coagulopathy, and acute renal failure. In addition to the liver phenotype, he had short stature and Pelger-Huët anomaly in the peripheral granulocytes...
2019: Human Genome Variation
https://read.qxmd.com/read/30534410/a-novel-intragenic-deletion-in-ophn1-in-a-japanese-patient-with-dandy-walker-malformation
#13
Aritoshi Iida, Eri Takeshita, Shunichi Kosugi, Yoichiro Kamatani, Yukihide Momozawa, Michiaki Kubo, Eiji Nakagawa, Kenji Kurosawa, Ken Inoue, Yu-Ichi Goto
Dandy-Walker malformation (DWM) is a rare congenital malformation defined by hypoplasia of the cerebellar vermis and cystic dilatation of the fourth ventricle. Oligophrenin-1 is mutated in X-linked intellectual disability with or without cerebellar hypoplasia. Here, we report a Japanese DWM patient carrying a novel intragenic 13.5-kb deletion in OPHN1 ranging from exon 11-15. This is the first report of an OPHN1 deletion in a Japanese patient with DWM.
2019: Human Genome Variation
https://read.qxmd.com/read/30455963/a-delayed-diagnosis-of-pallister-hall-syndrome-in-an-adult-male-following-the-incidental-detection-of-a-hypothalamic-hamartoma
#14
Eliza Courtney, Du Soon Swee, Diana Ishak, Joanne Ngeow
Pallister-Hall syndrome is a rare autosomal dominant condition that is associated with polydactyly and hypothalamic hamartoma and is caused predominantly by frameshift or nonsense pathogenic variants in the GLI3 gene. The majority of cases are identified during childhood; however, rare reports of diagnoses during adulthood exist. Here, we describe the identification of a novel nonsense GLI3 pathogenic variant in an adult male following the incidental detection of a hypothalamic hamartoma.
2018: Human Genome Variation
https://read.qxmd.com/read/30374406/a-novel-cul7-mutation-in-a-japanese-patient-with-3m-syndrome
#15
Tomozumi Takatani, Tadashi Shiohama, Rieko Takatani, Naoki Shimojo
3M syndrome is an autosomal recessive disease characterized by severe pre-natal and post-natal growth retardation, dysmorphic facial features, and skeletal abnormalities. We present a patient with 3M syndrome caused by the compound heterozygous mutations p.Trp68* and p.Gly1452Asp in CUL7 , the latter of which is novel, who exhibited a good body height response to growth hormone treatment. These results expand our knowledge of phenotype-genotype correlations in 3M syndrome, including correlations relevant to growth hormone response...
2018: Human Genome Variation
https://read.qxmd.com/read/30374405/eld-entropy-based-linkage-disequilibrium-index-between-multiallelic-sites
#16
Yukinori Okada
Quantification of linkage disequilibrium (LD) is a critical step in studies investigating human genome variations. Commonly used LD indices such as r 2 handle LD of biallelic variants for two sites. As shown in a previously introduced LD index of ε , normalized entropy difference of the haplotype frequency between LD and linkage equilibrium (LE) could be utilized to estimate LD of biallelic variants for multiple sites. Here, we developed eLD ( e ntropy-based L inkage D isequilibrium index between multiallelic sites) as publicly available software to calculate ε of multiallelic variants for two sites...
2018: Human Genome Variation
https://read.qxmd.com/read/30323943/exonic-deletions-in-galc-are-frequent-in-japanese-globoid-cell-leukodystrophy-patients
#17
Kaori Irahara-Miyana, Takashi Enokizono, Keiichi Ozono, Norio Sakai
Globoid-cell leukodystrophy is an autosomal-recessive lysosomal storage disorder. Single-base substitutions and small indel mutations in the GALC gene are common in Japanese patients. In this study, we identified three novel deletions, in exons 1, 8, and 11-12, in three patients using Multiplex Ligation-dependent Probe Amplification. We suggest that some patients in whom no or only a single pathogenic mutation is detected by Sanger sequencing may have exon deletions.
2018: Human Genome Variation
https://read.qxmd.com/read/30302266/exome-and-copy-number-variation-analyses-of-mayer-rokitansky-k%C3%A3-ster-hauser-syndrome
#18
Kazumi Takahashi, Takahide Hayano, Ryota Sugimoto, Hirofumi Kashiwagi, Mari Shinoda, Yoshihiro Nishijima, Takahiro Suzuki, Shingo Suzuki, Yuko Ohnuki, Akane Kondo, Takashi Shiina, Hirofumi Nakaoka, Ituro Inoue, Shun-Ichiro Izumi
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by congenital absence of the vagina and uterus. We conducted genome-wide SNP analyses and exome sequencing to detect the causes of MRKH syndrome. We identified de novo variants of MYCBP2 , NAV3 , and PTPN3 in three families and a variant of MYCBP2 in a sporadic case. Here, we demonstrated the partial genetic makeup of Japanese MRKH syndrome.
2018: Human Genome Variation
https://read.qxmd.com/read/30245840/long-range-haplotype-analysis-of-the-malaria-parasite-receptor-gene-ackr1-in-an-east-african-population
#19
Qinan Yin, Kshitij Srivastava, Amha Gebremedhin, Addisalem Taye Makuria, Willy Albert Flegel
The human ACKR1 gene encodes a glycoprotein expressing the Duffy blood group antigens (Fy). The Duffy protein acts as a receptor for distinct pro-inflammatory cytokines and malaria parasites. We determined the haplotypes of the ACKR1 gene in a population inhabiting a malaria-endemic area. We collected blood samples from 60 healthy volunteers in Ethiopia's southwestern low-altitude tropical region. An assay was devised to amplify the ACKR1 gene as a single amplicon and determine its genomic sequence. All haplotypes were resolved at 5178 nucleotides each, covering the coding sequence (CDS) of the ACKR1 gene and including the 5'- and 3'-untranslated regions (UTR), intron 1, and the 5'- and 3'-flanking regions...
2018: Human Genome Variation
https://read.qxmd.com/read/30210801/mitochondrial-dna-3243a-t-mutation-in-a-patient-with-melas-syndrome
#20
Takahiro Ikeda, Hitoshi Osaka, Hiroko Shimbo, Makiko Tajika, Masayo Yamazaki, Ayako Ueda, Kei Murayama, Takanori Yamagata
Approximately 80% of cases of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) harbor a heteroplasmic m.3243A>G transition in the tRNALeu (UUR) ( MTTL1 ) gene. We report a MELAS case with a rare heteroplasmic m.3243A>T mutation found by direct sequencing of MTTL1 . This mutation has been previously reported in 5 cases, of which 2 cases had the MELAS phenotype. Our case also strengthens the hypothesis that the m.3243A>T mutation can cause the MELAS phenotype.
2018: Human Genome Variation
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