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Human Mutation

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https://www.readbyqxmd.com/read/28337824/phenotype-genotype-correlations-of-pigo-deficiency-with-variable-phenotypes-from-infantile-lethality-to-mild-learning-difficulties
#1
Junpei Tanigawa, Haruka Mimatsu, Seiji Mizuno, Nobuhiko Okamoto, Daisuke Fukushi, Koji Tominaga, Hiroyuki Kidokoro, Yukako Muramatsu, Eriko Nishi, Shota Nakamura, Daisuke Motooka, Noriko Nomura, Kiyoshi Hayasaka, Tetsuya Niihori, Yoko Aoki, Shin Nabatame, Masahiro Hayakawa, Jun Natsume, Keiichi Ozono, Taroh Kinoshita, Nobuaki Wakamatsu, Yoshiko Murakami
Inherited GPI (glycosylphosphatidylinositol) deficiencies (IGDs), a recently defined group of diseases, show a broad spectrum of symptoms. Hyperphosphatasia mental retardation syndrome, also known as Mabry syndrome, is a type of IGDs. There are at least 26 genes involved in the biosynthesis and transport of GPI anchored proteins; however, IGDs constitute a rare group of diseases and correlations between the spectrum of symptoms and affected genes or the type of mutations have not been shown. Here we report four newly identified and five previously described Japanese families with PIGO (phosphatidylinositol glycan anchor biosynthesis class O) deficiency...
March 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28332257/exomic-variants-of-an-elderly-cohort-of-brazilians-in-the-abraom%C3%A2-database
#2
Michel Satya Naslavsky, Guilherme Lopes Yamamoto, Tatiana Ferreira de Almeida, Suzana A M Ezquina, Daniele Yumi Sunaga, Nam Pho, Daniel Bozoklian, Tatiana Orli Milkewitz Sandberg, Luciano Abreu Brito, Monize Lazar, Danilo Vicensotto Bernardo, Edson Amaro, Yeda A O Duarte, Maria Lúcia Lebrão, Maria Rita Passos-Bueno, Mayana Zatz
Brazilians are highly admixed with ancestry from Europe, Africa, America, and Asia yet still underrepresented in genomic databanks. We hereby present a collection of exomic variants from 609 elderly Brazilians in a census-based cohort (SABE609) with comprehensive phenotyping. Variants were deposited in ABraOM (Online Archive of Brazilian Mutations), a web-based public database. Population representative phenotype and genotype repositories are essential for variant interpretation through allele frequency filtering; since elderly individuals are less likely to harbor pathogenic mutations for early and adult-onset diseases, such variant databases are of great interest...
March 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28326637/purinergic-receptors-p2rx4-and-p2rx7-in-familial-multiple-sclerosis
#3
A Dessa Sadovnick, Ben J Gu, Anthony L Traboulsee, Cecily Q Bernales, Mary Encarnacion, Irene M Yee, Maria G Criscuoli, Xin Huang, Amber Ou, Carol J Milligan, Steven Petrou, James S Wiley, Carles Vilariño-Güell
Genetic variants in the purinergic receptors P2RX4 and P2RX7 have been shown to affect susceptibility to multiple sclerosis (MS). In this study we set out to evaluate whether rare coding variants of major effect could also be identified in these purinergic receptors. Sequencing analysis of P2RX4 and P2RX7 in 193 MS patients and 100 controls led to the identification of a rare three variant haplotype (P2RX7 rs140915863:C>T (p.T205M), P2RX7 rs201921967:A>G (p.N361S) and P2RX4 rs765866317:G>A (p.G135S)) segregating with disease in a multi-incident family with six family members diagnosed with MS (LOD = 3...
March 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28317323/a-functional-snp-regulated-by-mir-196a-3p-in-the-3-utr-of-fgf2-is-associated-with-bone-mineral-density-in-the-chinese-population
#4
Dong-Li Zhu, Yan Guo, Yan Zhang, Shan-Shan Dong, Wen Xu, Ruo-Han Hao, Xiao-Feng Chen, Han Yan, Shui-Yun Yang, Tie-Lin Yang
Previous studies have identified FGF2 as a susceptibility gene for osteoporosis in Caucasians. Evaluating the genetic associations in different ethnicities is necessary. Moreover, elucidating the functional mechanism for the susceptibility loci is important to offer new targets for therapeutic studies. Here, we genotyped ten SNPs in FGF2 and tested for associations with bone mineral density (BMD) in a discovery sample of 1300 Chinese subjects. Nominally significant results were subjected to replication in another sample of 1039 Chinese subjects...
March 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28276201/rare-deleterious-variants-in-grhl3-are-associated-with-human-spina-bifida
#5
Philippe Lemay, Patrizia De Marco, Alexandre Emond, Dan Spiegelman, Alexandre Dionne-Laporte, Sandra Laurent, Elisa Merello, Andrea Accogli, Guy A Rouleau, Valeria Capra, Zoha Kibar
Neural tube defects (NTDs), including spina bifida, are among the most common birth defects caused by failure of neural tube closure during development. They have a complex etiology involving largely undetermined environmental and genetic factors. Previous studies in mouse models have implicated the transcription factor Grhl3 as an important factor in the pathogenesis of spina bifida. In the present study, we conducted a re-sequencing analysis of GRHL3 in a cohort of 233 familial and sporadic cases of spina bifida...
March 8, 2017: Human Mutation
https://www.readbyqxmd.com/read/28271586/single-base-substitutions-in-the-chm-promoter-as-a-cause-of-choroideremia
#6
Alina Radziwon, Gavin Arno, Dianna Wheaton, Ellen M McDonagh, Emma L Baple, Kaylie Webb-Jones, David Birch, Andrew R Webster, Ian M MacDonald
Although over 150 unique mutations affecting the coding sequence of CHM have been identified in patients with the X-linked chorioretinal disease choroideremia (CHM), no regulatory mutations have been reported, and indeed the promoter has not been defined. Here we describe two independent families affected by CHM bearing a mutation outside the gene's coding region at position c.-98: C>A and C>T, which segregated with the disease. The male proband of family 1 was found to lack CHM mRNA and its gene product Rab escort protein 1 (REP-1), while whole genome sequencing of an affected male in family 2 excluded the involvement of any other known retinal genes...
March 8, 2017: Human Mutation
https://www.readbyqxmd.com/read/28256047/maternal-mutations-of-foxf1-cause-alveolar-capillary-dysplasia-despite-not-being-imprinted
#7
Miguel Alsina Casanova, Ana Monteagudo-Sánchez, Luciana Rodiguez Guerineau, Franck Court, Isabel Gazquez Serrano, Loreto Martorell, Carlota Rovira Zurriaga, Gudrun E Moore, Miho Ishida, Montserrat Castañon, Elisenda Moliner Calderon, David Monk, Julio Moreno Hernando
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare cause of pulmonary hypertension in newborns. Maternally inherited point mutations in Forkhead Box F1 gene (FOXF1), deletions of the gene, or its long-range enhancers on the maternal allele are responsible for this neonatal lethal disorder. Here, we describe monozygotic twins and one full-term newborn with ACD and gastrointestinal malformations caused by de novo mutations of FOXF1 on the maternal-inherited alleles. Since this parental transmission is consistent with genomic imprinting, the parent-of-origin specific monoallelic expression of genes, we have undertaken a detailed analysis of both allelic expression and DNA methylation...
March 3, 2017: Human Mutation
https://www.readbyqxmd.com/read/28251733/whole-transcriptome-sequencing-in-blood-provides-a-diagnosis-of-spinal-muscular-atrophy-with-progressive-myoclonic-epilepsy-sma-pme
#8
Kristin D Kernohan, Laure Frésard, Zachary Zappala, Taila Hartley, Kevin S Smith, Justin Wagner, Hongbin Xu, Arran McBride, Pierre R Bourque, Care Rare Canada Consortium, Steffany A L Bennett, David A Dyment, Kym M Boycott, Stephen B Montgomery, Jodi Warman-Chardon
At least 15% of disease-causing mutations affect mRNA splicing. Many splicing mutations are missed in a clinical setting due to limitations of in silico prediction algorithms or their location in non-coding regions. Whole transcriptome sequencing is a promising new tool to identify these mutations; however, it will be a challenge to obtain disease relevant tissue for RNA. Here, we describe an individual with a sporadic atypical spinal muscular atrophy, in whom clinical DNA sequencing reported one pathogenic ASAH1 mutation (c...
March 2, 2017: Human Mutation
https://www.readbyqxmd.com/read/28247525/mutation-in-mitochondrial-complex-iv-subunit-cox5a-causes-pulmonary-arterial-hypertension-lactic-acidemia-and-failure-to-thrive
#9
Fabian Baertling, Fathiya Al-Murshedi, Laura Sánchez-Caballero, Khalfan Al-Senaidi, Niranjan P Joshi, Hanka Venselaar, Mariël Am van den Brand, Leo Gj Nijtmans, Richard Jt Rodenburg
COX5A is a nuclear-encoded subunit of mitochondrial respiratory chain complex IV (cytochrome c oxidase). We present patients with a homozygous pathogenic variant in the COX5A gene. Clinical details of two affected siblings suffering from early-onset pulmonary arterial hypertension, lactic acidemia, failure to thrive and isolated complex IV deficiency are presented. We show that the variant lies within the evolutionarily conserved COX5A/COX4 interface domain, suggesting that it alters the interaction between these two subunits during complex IV biogenesis...
March 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28247551/characterization-of-chromosomal-abnormalities-in-pregnancy-losses-reveals-critical-genes-and-loci-for-human-early-development
#10
Yiyun Chen, Justin Bartanus, Desheng Liang, Hongmin Zhu, Amy M Breman, Janice L Smith, Hua Wang, Zhilin Ren, Ankita Patel, Pawel Stankiewicz, David S Cram, Sau Wai Cheung, Lingqian Wu, Fuli Yu
Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2186 product of conception (POC) samples were tested for copy number variations (CNVs) at two clinical diagnostic centers using whole genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets...
February 28, 2017: Human Mutation
https://www.readbyqxmd.com/read/28244183/nonketotic-hyperglycinemia-functional-assessment-of-missense-variants-in-gldc-to-understand-phenotypes-of-the-disease
#11
Irene Bravo-Alonso, Rosa Navarrete, Laura Arribas-Carreira, Almudena Perona, David Abia, María Luz Couce, Angels García-Cazorla, Ana Morais, Rosario Domingo, María Antonia Ramos, Michael A Swanson, Johan L K Van Hove, Magdalena Ugarte, Belén Pérez, Celia Pérez-Cerdá, Pilar Rodríguez-Pombo
The rapid analysis of genomic data is providing effective mutational confirmation in patients with clinical and biochemical hallmarks of a specific disease. This is the case for Nonketotic Hyperglycinemia (NKH), a Mendelian disorder causing seizures in neonates and early-infants, primarily due to mutations in the GLDC gene. However, understanding the impact of missense-variants identified in this gene is a major challenge for the application of genomics into clinical practice. Herein, a comprehensive functional and structural analysis of 19 GLDC missense-variants identified in a cohort of 26 NKH patients was performed...
February 28, 2017: Human Mutation
https://www.readbyqxmd.com/read/28236339/mutations-of-the-aminoacyl-trna-synthetases-sars-and-wars2-are-implicated-in-the-aetiology-of-autosomal-recessive-intellectual-disability
#12
Luciana Musante, Lucia Püttmann, Kimia Kahrizi, Masoud Garshasbi, Hao Hu, Henning Stehr, Bettina Lipkowitz, Sabine Otto, Lars R Jensen, Andreas Tzschach, Payman Jamali, Thomas Wienker, Hossein Najmabadi, Hans Hilger Ropers, Andreas W Kuss
Intellectual disability (ID) is the hallmark of an extremely heterogeneous group of disorders that comprises a wide variety of syndromic and non-syndromic phenotypes. Here we report on mutations in two aminoacyl-tRNA synthetases that are associated with ID in two unrelated Iranian families. In the first family, we identified a homozygous missense mutation (c.514G>A, p.Asp172Asn) in the cytoplasmic seryl-tRNA synthetase (SARS) gene. The mutation affects the enzymatic core domain of the protein and impairs its enzymatic activity, probably leading to reduced cytoplasmic tRNA(Ser) concentrations...
February 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28236343/tarseqqc-quality-control-on-targeted-sequencing-experiments-in-r
#13
Gabriela A Merino, Yanina A Murua, Cristóbal Fresno, Juan M Sendoya, Mariano Golubicki, Soledad Iseas, Mariana Coraglio, Osvaldo L Podhajcer, Andrea S Llera, Elmer A Fernández
Targeted sequencing is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, under-covered relevant clinical variants may not be reported, impacting on pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions...
February 24, 2017: Human Mutation
https://www.readbyqxmd.com/read/28236341/ednrb-mutations-cause-waardenburg-syndrome-type-ii-in-the-heterozygous-state
#14
Sarah Issa, Nadege Bondurand, Emmanuelle Faubert, Sylvain Poisson, Laure Lecerf, Patrick Nitschke, Naima Deggouj, Natalie Loundon, Laurence Jonard, Albert David, Yves Sznajer, Patricia Blanchet, Sandrine Marlin, Veronique Pingault
Waardenburg syndrome (WS) is a genetic disorder characterized by sensorineural hearing loss and pigmentation anomalies. The clinical definition of four WS types is based on additional features due to defects in structures mostly arising from the neural crest, with type I and type II being the most frequent. While type I is tightly associated to PAX3 mutations, WS type II (WS2) remains partly enigmatic with mutations in known genes (MITF, SOX10) accounting for only 30% of the cases. We performed exome sequencing in a WS2 index case and identified a heterozygous missense variation in EDNRB...
February 24, 2017: Human Mutation
https://www.readbyqxmd.com/read/28230923/predicting-phenotype-from-genotype-improving-accuracy-through-more-robust-experimental-and-computational-modeling
#15
Jonathan Gallion, Amanda Koire, Panagiotis Katsonis, Anne-Marie Schoenegge, Michel Bouvier, Olivier Lichtarge
Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions...
February 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229513/pathogenic-asxl1-somatic-variants-in-reference-databases-complicate-germline-variant-interpretation-for-bohring-opitz-syndrome
#16
Colleen M Carlston, Anne H O'Donnell-Luria, Hunter R Underhill, Beryl B Cummings, Ben Weisburd, Eric V Minikel, Daniel P Birnbaum, Tatiana Tvrdik, Daniel G MacArthur, Rong Mao
The clinical interpretation of genetic variants has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC) database. Pathogenic variants in genes associated with severe, pediatric-onset, highly penetrant, autosomal dominant conditions are assumed to be absent or rare in these databases. Exome sequencing of a six-year-old female patient with seizures, developmental delay, dysmorphic features and failure to thrive identified an ASXL1 variant previously reported as causative of Bohring-Opitz syndrome (BOS)...
February 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229514/mutations-in-genes-encoding-polycomb-repressive-complex-2-subunits-cause-weaver-syndrome
#17
Eri Imagawa, Ken Higashimoto, Yasunari Sakai, Chikahiko Numakura, Nobuhiko Okamoto, Satoko Matsunaga, Akihide Ryo, Yoshinori Sato, Masafumi Sanefuji, Kenji Ihara, Yui Takada, Gen Nishimura, Hirotomo Saitsu, Takeshi Mizuguchi, Satoko Miyatake, Mitsuko Nakashima, Noriko Miyake, Hidenobu Soejima, Naomichi Matsumoto
Weaver syndrome is a rare congenital overgrowth disorder caused by heterozygous mutations in EZH2 (enhancer of zeste homolog 2) or EED (embryonic ectoderm development). EZH2 and EED are core components of the polycomb repressive complex 2 (PRC2), which possesses histone methyltransferase activity and catalyzes trimethylation of histone H3 at lysine 27. Here, we analyzed eight probands with clinically suspected Weaver syndrome by whole exome sequencing and identified three mutations: a 25.4-kb deletion partially involving EZH2 and CUL1 (individual 1), a missense mutation (c...
February 22, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229507/a-samhd1-mutation-associated-with-aicardi-gouti%C3%A3-res-syndrome-uncouples-the-ability-of-samhd1-to-restrict-hiv-1-from-its-ability-to-downmodulate-type-i-interferon-in-humans
#18
Tommy E White, Alberto Brandariz-Nuñez, Alicia Martinez-Lopez, Caitlin Knowlton, Gina Lenzi, Baek Kim, Dmitri Ivanov, Felipe Diaz-Griffero
Mutations in the human SAMHD1 gene are known to correlate with the development of the Aicardi-Goutières Syndrome (AGS), which is an inflammatory encephalopathy that exhibits neurological dysfunction characterized by increased production of type I interferon (IFN); this evidence has lead to the concept that the SAMHD1 protein negatively regulates the type I IFN response. Additionally, the SAMHD1 protein has been shown to prevent efficient HIV-1 infection of macrophages, dendritic cells and resting CD4+ T cells...
February 22, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229505/a-variant-in-a-cis-regulatory-element-enhances-claudin-14-expression-and-is-associated-with-pediatric-onset-hypercalciuria-and-kidney-stones
#19
Megan E Ure, Emma Heydari, Wanling Pan, Ajay Ramesh, Sabah Rehman, Catherine Morgan, Maury Pinsk, Robin Erickson, Johannes M Herrmann, Henrik Dimke, Emmanuelle Cordat, Mathieu Lemaire, Michael Walter, R Todd Alexander
The greatest risk factor for kidney stones is hypercalciuria, the etiology of which is largely unknown. A recent genome-wide association study (GWAS) linked hypercalciuria and kidney stones to a claudin-14 (CLDN14) risk haplotype. However, the underlying molecular mechanism was not delineated. Recently, renal CLDN14 expression was found to increase in response to increased plasma calcium, thereby inducing calciuria. We hypothesized therefore that some children with hypercalciuria and kidney stones harbor a CLDN14 variant that inappropriately increases gene expression...
February 22, 2017: Human Mutation
https://www.readbyqxmd.com/read/28224672/pon-p-and-pon-p2-predictor-performance-in-cagi-challenges-lessons-learned
#20
Abhishek Niroula, Mauno Vihinen
Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed towards the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools...
February 22, 2017: Human Mutation
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