A novel FBXO28 frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41-q42 deletion phenotype.

Am J Med Genet A. 2018 Jul;176(7):1549-1558

Authors: Balak C, Belnap N, Ramsey K, Joss S, Devriendt K, Naymik M, Jepsen W, Siniard AL, Szelinger S, Parker ME, Richholt R, Izatt T, LaFleur M, Terraf P, Llaci L, De Both M, Piras IS, Rangasamy S, Schrauwen I, Craig DW, Huentelman M, Narayanan V

Abstract
Chromosome 1q41-q42 deletions have recently been associated with a recognizable neurodevelopmental syndrome of early childhood (OMIM 612530). Within this group, a predominant phenotype of developmental delay (DD), intellectual disability (ID), epilepsy, distinct dysmorphology, and brain anomalies on magnetic resonance imaging/computed tomography has emerged. Previous reports of patients with de novo deletions at 1q41-q42 have led to the identification of an evolving smallest region of overlap which has included several potentially causal genes including DISP1, TP53BP2, and FBXO28. In a recent report, a cohort of patients with de novo mutations in WDR26 was described that shared many of the clinical features originally described in the 1q41-q42 microdeletion syndrome (MDS). Here, we describe a novel germline FBXO28 frameshift mutation in a 3-year-old girl with intractable epilepsy, ID, DD, and other features which overlap those of the 1q41-q42 MDS. Through a familial whole-exome sequencing study, we identified a de novo FBXO28 c.972_973delACinsG (p.Arg325GlufsX3) frameshift mutation in the proband. The frameshift and resulting premature nonsense mutation have not been reported in any genomic database. This child does not have a large 1q41-q42 deletion, nor does she harbor a WDR26 mutation. Our case joins a previously reported patient also in whom FBXO28 was affected but WDR26 was not. These findings support the idea that FBXO28 is a monogenic disease gene and contributes to the complex neurodevelopmental phenotype of the 1q41-q42 gene deletion syndrome.

PMID: 30160831 [PubMed - in process]

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies.

Genet Med. 2018 Aug 30;:

Authors: Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, DDD Study, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P

Abstract
PURPOSE: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.
METHODS: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.
RESULTS: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.
CONCLUSION: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

PMID: 30158690 [PubMed - as supplied by publisher]

Neurodegeneration in an adolescent with Sjogren-Larsson syndrome: a decade-long follow-up case report.

BMC Med Genet. 2018 Aug 29;19(1):152

Authors: Cho KH, Shim SH, Jung Y, Sung SR, Kim M

Abstract
BACKGROUND: Sjogren-Larsson syndrome is a hereditary neurocutaneous syndrome that is non-progressive in nature. Although neuroregression has been reported in seizure-prone preschool children requiring anti-epileptic treatment, teenage-onset dystonia precipitating neurodegeneration without any immediate causal events has yet to be reported.
CASE PRESENTATION: We describe a young woman with spastic diplegia and intellectual disability who began to show progressive neurological deterioration from 12 years of age, with the onset of dystonia and tremor. She was initially diagnosed with spastic cerebral palsy and periventricular leukomalacia based on brain magnetic resonance imaging. Follow-up brain imaging from 13 years of age did not reveal apparent changes, though abnormal electroencephalographic findings occurred in parallel with her decline in motor function. By 19 years of age, she had developed dysphagia and became completely dependent on others for most activities of daily living. Ultimately, whole-exome sequencing revealed a heterozygous compound mutation in the ALDH3A2 gene that corresponds to Sjogren-Larsson syndrome: an exon 9 deletion (1291-1292delAA) from the mother and an exon 5 splicing mutation (798 + 1delG) from the father. Neuroregression has been reported in preschool children after seizures requiring treatment, though our patient did not experience any immediate causal events. This report summarizes the clinical, radiologic, and electrophysiological findings observed over a decade concurrent with neurological deterioration after the onset of dystonia and tremor at the age of developmental ceiling in Sjogren-Larsson syndrome.
CONCLUSIONS: In addition to the influence of additive variants or other environmental factors, accumulation of metabolites due to defective fatty aldehyde dehydrogenase is a potential pathomechanism of neurodegeneration in this patient. Neurological deterioration may be a presentation that is unnoticed in Sjogren-Larsson syndrome due to the rarity of the disease. This report highlights a unique clinical feature of Sjogren-Larsson syndrome with progressive neurodegeneration associated with dystonia and tremor.

PMID: 30157790 [PubMed - in process]

Patient with a novel purine-rich element binding protein A mutation.

Congenit Anom (Kyoto). 2017 Nov;57(6):201-204

Authors: Okamoto N, Nakao H, Niihori T, Aoki Y

Abstract
There have been several reports on 5q31.3 microdeletion syndrome. The overlapping deleted region includes purine-rich element binding protein A (PURA), which encodes transcriptional activator protein Pur-α. Patients with PURA mutations show moderate to severe neurodevelopmental delay and learning disability. Neonatal hypotonia, respiratory insufficiency, feeding difficulties, and seizures are often seen. Dysmorphic features including myopathic faces are helpful as clinical signs of the diagnosis. We report a patient with a novel PURA mutation detected by whole-exome sequencing. We suggest that PURA abnormality is a recognizable syndrome.

PMID: 28164378 [PubMed - indexed for MEDLINE]

Variable cardiovascular phenotypes associated with SMAD2 pathogenic variants.

Hum Mutat. 2018 Aug 29;:

Authors: Granadillo JL, Chung WK, Hecht L, Corsten-Janssen N, Wegner D, Bijvank SWAN, Toler TL, Pineda-Alvarez DE, Douglas G, Murphy JJ, Shimony J, Shinawi M

Abstract
SMAD2 is a downstream effector in the TGF-β signaling pathway, which is important for pattern formation and tissue differentiation. Pathogenic variants in SMAD2 have been reported in association with arterial aneurysms and dissections and in large cohorts of subjects with complex congenital heart disease (CHD). We used whole exome sequencing (WES) to investigate the molecular cause of CHD and other congenital anomalies in three probands and of an arterial aneurysm in an additional patient. Patient 1 and 2 presented with complex CHD, developmental delay, seizures, dysmorphic features, short stature and poor weight gain. Patient 3 was a fetus with complex CHD and heterotaxy. The fourth patient is an adult female with aortic root aneurysm and physical features suggestive of a connective tissue disorder. WES identified pathogenic truncating variants, a splice variant, and a predicted deleterious missense variant in SMAD2. We compare the phenotypes and genotypes in our patients with previously reported cases. Our data suggest two distinct phenotypes associated with pathogenic variants in SMAD2: complex CHD with or without laterality defects and other congenital anomalies, and a late-onset vascular phenotype characterized by arterial aneurysms with connective tissue abnormalities. This article is protected by copyright. All rights reserved.

PMID: 30157302 [PubMed - as supplied by publisher]

Whole exome sequencing in Finnish families identifies new candidate genes for osteoarthritis.

PLoS One. 2018;13(8):e0203313

Authors: Skarp S, Kämäräinen OP, Wei GH, Jakkula E, Kiviranta I, Kröger H, Auvinen J, Lehenkari P, Ala-Kokko L, Männikkö M

Abstract
INTRODUCTION: Osteoarthritis (OA) is the most common degenerative joint disease and one of the major causes of disability worldwide. It is a multifactorial disorder with a significant genetic component. The heritability of OA has been estimated to be 60% for hip OA and 39% for knee OA. Genetic factors behind OA are still largely unknown. Studying families with strong history of OA, facilitates examining the co-segregation of genetic variation and OA. The aim of this study was to identify new, rare genetic factors and novel candidate genes for OA.
METHODS: Eight patients from three Finnish families with hip and knee OA were studied using whole exome sequencing. We focused on rare exonic variants with predicted pathogenicity and variants located in active promoter or strong enhancer regions. Expression of identified candidate genes were studied in bone and cartilage tissues and the observed variants were investigated using bioinformatic analyses.
RESULTS: Two rare variants co-segregated with OA in two families. In Family 8 a missense variant (c.628C>G, p.Arg210Gly) was observed in the OLIG3 gene that encodes a transcription factor known to be associated with rheumatoid arthritis and inflammatory polyarthritis. The Arg210Gly variant was estimated to be pathogenic by Polyphen-2 and Mutation taster and the locus is conserved among mammals. In Family 12 the observed variant (c.-127G>T) was located in the transcription start site of the FIP1L1 gene. FIP1L1 participates in the regulation of polyadenylation. The c.-127G>T is located in the transcription start site and may alter the DNA-binding of transcription factors. Both, OLIG3 and FIP1L1 were observed in human bone and cartilage.
CONCLUSION: The identified variants revealed novel candidate genes for OA. OLIG3 and FIP1L1 have specific roles in transcription and may effect expression of other genes. Identified variants in these genes may thus have a role in the regulatory events leading to OA.

PMID: 30157244 [PubMed - in process]

A Rare Case of Severe Congenital RYR1-Associated Myopathy.

Case Rep Genet. 2018;2018:6184185

Authors: Laforgia N, Capozza M, De Cosmo L, Di Mauro A, Baldassarre ME, Mercadante F, Torella AL, Nigro V, Resta N

Abstract
Congenital myopathies are a group of rare inherited diseases, defined by hypotonia and muscle weakness. We report clinical and genetic characteristics of a male preterm newborn, whose phenotype was characterized by severe hypotonia and hyporeactivity, serious respiratory distress syndrome that required mechanical ventilation, clubfoot, and other dysmorphic features. The diagnostic procedure was completed with the complete exome sequencing of the proband and of his parents and his sister, which showed new mutations in the ryanodine receptor gene (RYR1), which maps to chromosome 19q13.2 and encodes the skeletal muscle isoform of a calcium-release channel in the sarcoplasmic reticulum (RyR1). This report confirms that early diagnosis and accurate study of genomic disorders are very important, enabling proper genetic counselling of the reproductive risk, as well as disease prognosis and patient management.

PMID: 30155320 [PubMed]

Insights Into de novo Mutation Variation in Lithuanian Exome.

Front Genet. 2018;9:315

Authors: Pranckėnienė L, Jakaitienė A, Ambrozaitytė L, Kavaliauskienė I, Kučinskas V

Abstract
In the last decade, one of the biggest challenges in genomics research has been to distinguish definitive pathogenic variants from all likely pathogenic variants identified by next-generation sequencing. This task is particularly complex because of our lack of knowledge regarding overall genome variation and pathogenicity of the variants. Therefore, obtaining sufficient information about genome variants in the general population is necessary as such data could be used for the interpretation of de novo mutations (DNMs) in the context of patient's phenotype in cases of sporadic genetic disease. In this study, data from whole-exome sequencing of the general population in Lithuania were directly examined. In total, 84 (VarScan) and 95 (VarSeqTM) DNMs were identified and validated using different algorithms. Thirty-nine of these mutations were considered likely to be pathogenic based on gene function, evolutionary conservation, and mutation impact. The mutation rate estimated per position pair per generation was 2.74 × 10-8 [95% CI: 2.24 × 10-8-3.35 × 10-8] (VarScan) and 2.4 × 10-8 [95% CI: 1.96 × 10-8-2.99 × 10-8] (VarSeqTM), with 1.77 × 10-8 [95% CI: 6.03 × 10-9-5.2 × 10-8] de novo indels per position per generation. The rate of germline DNMs in the Lithuanian population and the effects of the genomic and epigenetic context on DNM formation were calculated for the first time in this study, providing a basis for further analysis of DNMs in individuals with genetic diseases. Considering these findings, additional studies in patient groups with genetic diseases with unclear etiology may facilitate our ability to distinguish certain pathogenic or adaptive DNMs from tolerated background DNMs and to reliably identify disease-causing DNMs by their properties through direct observation.

PMID: 30154829 [PubMed]

Vasculitis Pathogenesis: Can We Talk About Precision Medicine?

Front Immunol. 2018;9:1892

Authors: Ozen S, Batu ED

Abstract
Precision medicine is designing the medical care by taking into account the individual variability for each person. We have tried to address whether the existing data may guide precision medicine in primary systemic vasculitides (PSV). We have reviewed genome-wide association studies (GWAS) data, lessons from monogenic mimics of these diseases, and biomarker studies in immunoglobulin A vasculitis/Henoch-Schönlein purpura, Kawasaki disease, anti-neutrophil cytoplasmic antibody-associated vasculitis, polyarteritis nodosa (PAN), Takayasu arteritis, and Behçet's disease (BD). GWAS provide insights about the pathogenesis of PSV while whole exome sequencing studies lead to discovery of monogenic vasculitides, phenotype of which could mimic other types of vasculitis such as PAN and BD. Monogenic vasculitides form a subgroup of vasculitis which are caused by single gene alterations and discovery of these diseases has enabled more specific therapies in these patients. With increasing number of studies on biomarkers, new targets for treatment appear and better and structured follow-up of PSV patients will become possible. Proteomics and metabolomics studies are required to better categorize our patients with PSV so that we can manage them appropriately and offer more targeted therapy.

PMID: 30154798 [PubMed - in process]

Analysis of cancer genomes reveals basic features of human aging and its role in cancer development.

Nat Commun. 2016 08 12;7:12157

Authors: Podolskiy DI, Lobanov AV, Kryukov GV, Gladyshev VN

Abstract
Somatic mutations have long been implicated in aging and disease, but their impact on fitness and function is difficult to assess. Here by analysing human cancer genomes we identify mutational patterns associated with aging. Our analyses suggest that age-associated mutation load and burden double approximately every 8 years, similar to the all-cause mortality doubling time. This analysis further reveals variance in the rate of aging among different human tissues, for example, slightly accelerated aging of the reproductive system. Age-adjusted mutation load and burden correlate with the corresponding cancer incidence and precede it on average by 15 years, pointing to pre-clinical cancer development times. Behaviour of mutation load also exhibits gender differences and late-life reversals, explaining some gender-specific and late-life patterns in cancer incidence rates. Overall, this study characterizes some features of human aging and offers a mechanism for age being a risk factor for the onset of cancer.

PMID: 27515585 [PubMed - indexed for MEDLINE]

Novel compound heterozygous EPG5 mutations consisted with a missense mutation and a microduplication in the exon 1 region identified in a Japanese patient with Vici syndrome.

Am J Med Genet A. 2018 Aug 27;:

Authors: Shimada S, Hirasawa K, Takeshita A, Nakatsukasa H, Yamamoto-Shimojima K, Imaizumi T, Nagata S, Yamamoto T

Abstract
Vici syndrome is a rare, autosomal recessive, multisystem disorder, characterized by agenesis of the corpus callosum, cataracts, psychomotor delay, cardiomyopathy, hypopigmentation, and recurrent infections. Mutations in the ectopic P-granules autophagy protein 5 homolog gene (EPG5), which encodes a key autophagy regulator, are responsible for this syndrome. A 3-year-old Japanese girl manifesting similar symptoms to those found in patients with Vici syndrome showed intractable diarrhea, rather than immunodeficiency. Whole exome sequencing identified only a heterozygous variant in EPG5, NM_020964.2(EPG5):c.3389A > C (p.His1130Pro), which was inherited from her mother. Sequencing analyses of the EPG5 messenger RNA showed only an altered nucleotide "C" at position, c.3389, indicating decreased expression of the wild-type allele. Microarray-based comparative genomic hybridization revealed a de novo microduplication in the exon 1 region. Large exon deletions and duplications of EPG5 have never been reported so far. This was considered the cause of the decreased expression of the wild-type allele. In conclusion, we successfully identified novel compound heterozygous mutations in EPG5 in a patient who was clinically considered to have Vici syndrome.

PMID: 30152144 [PubMed - as supplied by publisher]

De novo variant in KIF26B is associated with pontocerebellar hypoplasia with infantile spinal muscular atrophy.

Am J Med Genet A. 2018 Aug 27;:

Authors: Wojcik MH, Okada K, Prabhu SP, Nowakowski DW, Ramsey K, Balak C, Rangasamy S, Brownstein CA, Schmitz-Abe K, Cohen JS, Fatemi A, Shi J, Grant EP, Narayanan V, Ho HH, Agrawal PB

Abstract
KIF26B is a member of the kinesin superfamily with evolutionarily conserved functions in controlling aspects of embryogenesis, including the development of the nervous system, though its function is incompletely understood. We describe an infant with progressive microcephaly, pontocerebellar hypoplasia, and arthrogryposis secondary to the involvement of anterior horn cells and ventral (motor) nerves. We performed whole exome sequencing on the trio and identified a de novo KIF26B missense variant, p.Gly546Ser, in the proband. This variant alters a highly conserved amino acid residue that is part of the phosphate-binding loop motif and motor-like domain and is deemed pathogenic by several in silico methods. Functional analysis of the variant protein in cultured cells revealed a reduction in the KIF26B protein's ability to promote cell adhesion, a defect that potentially contributes to its pathogenicity. Overall, KIF26B may play a critical role in the brain development and, when mutated, cause pontocerebellar hypoplasia with arthrogryposis.

PMID: 30151950 [PubMed - as supplied by publisher]

CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis.

Methods Mol Biol. 2018;1865:163-174

Authors: Deniz E, Mis EK, Lane M, Khokha MK

Abstract
In the US and Europe, birth defects are the leading cause of infant mortality. Among birth defects, Congenital Heart Disease (CHD) occurs in approximately 8 out of 1000 live births, affects 1.3 million newborns per year worldwide, and has the highest mortality rate. While there is evidence to indicate that CHD does have a genetic basis, most of the CHD burden remains unexplained genetically. Fortunately, new genomics technologies are enabling genetic analyses of CHD patients. Whole exome sequencing of trios as well as copy number variations assayed by high-density SNP arrays can now be obtained at high efficiency and relatively low cost. These efforts are identifying a number of sequence variations in patients with CHD, but only a small percentage have second unrelated alleles to validate them as disease causing. Importantly, most of these candidate genes do not have an identified molecular mechanism implicating them in cardiac development. Therefore, there is a pressing need to develop rapid functional assays to evaluate candidate genes for a role in cardiac development, and then to investigate the underlying developmental mechanisms. Most recently, the advent of CRISPR/Cas9 genome editing technology has greatly enhanced the ability to manipulate and observe the function of the genome in model systems and cell culture. Incorporating the power of a developmental system such as Xenopus tropicalis with the CRISPR/Cas9 system and the microscale imaging modality optical coherence tomography (OCT), the analysis of thousands of different genes in cardiac development becomes possible.

PMID: 30151766 [PubMed - in process]

Saphenous vein graft aneurysm formation in a patient with idiopathic multiple aneurysms.

J Vasc Surg Cases Innov Tech. 2018 Sep;4(3):197-200

Authors: Lun Y, Jiang H, Jing Y, Xin S, Zhang J

Abstract
True aneurysmal vein graft dilation is rare, and its etiology remains speculative. However, systemic dilation diathesis is regarded as a risk factor. We herein report a case of a rapidly expanding aneurysm in a great saphenous vein graft, resulting in distal malperfusion in a patient who had previously undergone open repair of multiple popliteal artery aneurysms. After an unsuccessful endovascular intervention, the dilated section was eventually replaced by a reversed segment of the contralateral great saphenous vein. Subsequent whole-exome sequencing identified no relevant mutations. This case provides further evidence that aneurysmal disease may be associated with systemic dilation diathesis.

PMID: 30148238 [PubMed]

Genetic screening of regulatory regions of pituitary transcription factors in patients with idiopathic pituitary hormone deficiencies.

Pituitary. 2018 Feb;21(1):76-83

Authors: Elizabeth M, Hokken-Koelega ACS, Schuilwerve J, Peeters RP, Visser TJ, de Graaff LCG

Abstract
PURPOSE: Mutation frequencies of PROP1, POU1F1 and HESX1 in patients with combined pituitary hormone deficiencies (CPHD) vary substantially between populations. They are low in sporadic CPHD patients in Western Europe. However, most clinicians still routinely send DNA of their CPHD patients for genetic screening of these pituitary transcription factors. Before we can recommend against screening of PROP1, POU1F1 and HESX1 as part of routine work-up for Western-European sporadic CPHD patients, it is crucial to rule out possible defects in regulatory regions of these genes, which could also disturb the complex process of pituitary organogenesis.
METHODS: The regulatory regions of PROP1, POU1F1 and HESX1 are not covered by Whole Exome Sequencing as they are largely located outside the coding regions. Therefore, we manually sequenced the regulatory regions, previously defined in the literature, of PROP1, POU1F1 and HESX1 among 88 Dutch patients with CPHD. We studied promoter SNPs in relation to phenotypic data.
RESULTS: We found six known SNPs in the PROP1 promoter. In the POU1F1 promoter, we found one new variant and two known SNPs. We did not find any variant in the HESX1 promoter.
CONCLUSION: Although the new POU1F1 variant might explain the phenotype of one patient, the general conclusion of this study is that variants in regulatory regions of PROP1, POU1F1 and HESX1 are rare in patients with sporadic CPHD in the Netherlands. We recommend that genetic screening of these pituitary transcription factors should no longer be part of routine work-up for Western-European, and especially Dutch, sporadic CPHD patients.

PMID: 29255988 [PubMed - indexed for MEDLINE]

De novo genic mutations among a Chinese autism spectrum disorder cohort.

Nat Commun. 2016 11 08;7:13316

Authors: Wang T, Guo H, Xiong B, Stessman HA, Wu H, Coe BP, Turner TN, Liu Y, Zhao W, Hoekzema K, Vives L, Xia L, Tang M, Ou J, Chen B, Shen Y, Xun G, Long M, Lin J, Kronenberg ZN, Peng Y, Bai T, Li H, Ke X, Hu Z, Zhao J, Zou X, Xia K, Eichler EE

Abstract
Recurrent de novo (DN) and likely gene-disruptive (LGD) mutations contribute significantly to autism spectrum disorders (ASDs) but have been primarily investigated in European cohorts. Here, we sequence 189 risk genes in 1,543 Chinese ASD probands (1,045 from trios). We report an 11-fold increase in the odds of DN LGD mutations compared with expectation under an exome-wide neutral model of mutation. In aggregate, ∼4% of ASD patients carry a DN mutation in one of just 29 autism risk genes. The most prevalent gene for recurrent DN mutations is SCN2A (1.1% of patients) followed by CHD8, DSCAM, MECP2, POGZ, WDFY3 and ASH1L. We identify novel DN LGD recurrences (GIGYF2, MYT1L, CUL3, DOCK8 and ZNF292) and DN mutations in previous ASD candidates (ARHGAP32, NCOR1, PHIP, STXBP1, CDKL5 and SHANK1). Phenotypic follow-up confirms potential subtypes and highlights how large global cohorts might be leveraged to prove the pathogenic significance of individually rare mutations.

PMID: 27824329 [PubMed - indexed for MEDLINE]

BAG3 mutation in a patient with atypical phenotypes of myofibrillar myopathy and Charcot-Marie-Tooth disease.

Genes Genomics. 2018 Aug 25;:

Authors: Kim SJ, Nam SH, Kanwal S, Nam DE, Yoo DH, Chae JH, Suh YL, Chung KW, Choi BO

Abstract
Bcl2-associated athanogene 3 (BAG3) mutations have been reported to cause the myofibrillar myopathy (MFM) which shows progressive limb muscle weakness, respiratory failure, and cardiomyopathy. Myopathy patients with BAG3 mutation are very rare. We described a patient showing atypical phenotypes. We aimed to find the genetic cause of Korean patients with sensory motor polyneuropathy, myopathy and rigid spine. We performed whole exome sequencing (WES) with 423 patients with sensory motor polyneuropathy. We found BAG3 mutation in one patient with neuropathy, myopathy and rigid spine syndrome, and performed electrophysiological study, whole body MRI and muscle biopsy on the patient. A de novo heterozygous p.Pro209Leu (c.626C>T) mutation in BAG3 was identified in a female myopathy. She first noticed a gait disturbance and spinal rigidity at the age of 11, and serum creatine kinase levels were elevated ninefolds than normal. She showed an axonal sensory-motor polyneuropathy like Charcot-Marie-Tooth disease (CMT), myopathy, rigid spine and respiratory dysfunction; however, she did not show any cardiomyopathy, which is a common symptom in BAG3 mutation. Lower limb MRI and whole spine MRI showed bilateral symmetric fatty atrophy of muscles at the lower limb and paraspinal muscles. When we track traceable MRI 1 year later, the muscle damage progressed slowly. As far as our knowledge, this is the first Korean patient with BAG3 mutation. We described a BAG3 mutation patient with atypical phenotype of CMT and myopathy, and those are expected to broaden the clinical spectrum of the disease and help to diagnose it.

PMID: 30145633 [PubMed - as supplied by publisher]

Exome sequencing identifies a novel frameshift variant causing hypomagnesemia with secondary hypocalcemia.

CEN Case Rep. 2018 Aug 24;:

Authors: Azim MK, Mehnaz A, Ahmed JZ, Mujtaba G

Abstract
Hypomagnesemia with secondary hypocalcemia is a rare autosomal-recessive disorder characterized by intense hypomagnesemia associated with hypocalcemia (HSH). Mutations in the TRPM6 gene, encoding the epithelial Mg2+ channel TRPM6, have been proven to be the molecular cause of this disease. This study identified causal mutations in a 2-month-old male patient of hypomagnesemia from a consanguineous marriage. Biochemical analyses indicated the diagnosis of HSH due to primary gastrointestinal loss of magnesium. Whole exome sequencing of the trio (i.e. proband and both parents) was carried out with mean coverage of > 150×. ANNOVAR was used to annotate functional consequences of genetic variation from exome sequencing data. After variant filtering and annotation, a number of single nucleotide variants (SNVs) and 2 bp deletion at exon26:c.4402_4403delCT in TRPM6 gene were identified. This deletion which resulted in a novel frameshift mutation in exon 26 of this gene was confirmed by Sanger sequencing. With these investigations in hand, the patient was managed with magnesium sulphate. The patient remained asymptomatic and was developmentally and neurologically normal till his last follow up.

PMID: 30144020 [PubMed - as supplied by publisher]

Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract.

J Am Soc Nephrol. 2018 Aug 24;:

Authors: van der Ven AT, Connaughton DM, Ityel H, Mann N, Nakayama M, Chen J, Vivante A, Hwang DY, Schulz J, Braun DA, Schmidt JM, Schapiro D, Schneider R, Warejko JK, Daga A, Majmundar AJ, Tan W, Jobst-Schwan T, Hermle T, Widmeier E, Ashraf S, Amar A, Hoogstraaten CA, Hugo H, Kitzler TM, Kause F, Kolvenbach CM, Dai R, Spaneas L, Amann K, Stein DR, Baum MA, Somers MJG, Rodig NM, Ferguson MA, Traum AZ, Daouk GH, Bogdanović R, Stajić N, Soliman NA, Kari JA, El Desoky S, Fathy HM, Milosevic D, Al-Saffar M, Awad HS, Eid LA, Selvin A, Senguttuvan P, Sanna-Cherchi S, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Wilson MW, Mane SM, Lifton RP, Lee RS, Bauer SB, Lu W, Reutter HM, Tasic V, Shril S, Hildebrandt F

Abstract
BACKGROUND: Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12% of patients with CAKUT.
METHODS: We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT.
RESULTS: In 29 families (13%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient's CAKUT phenotype. In three families (1%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8%).
CONCLUSIONS: We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.

PMID: 30143558 [PubMed - as supplied by publisher]

First Korean Case of Renpenning Syndrome with Novel Mutation in PQBP1 Diagnosed by Targeted Exome Sequencing, and Literature Review.

Ann Clin Lab Sci. 2018 Jul;48(4):522-527

Authors: Jeong HI, Yang A, Kim J, Jang JH, Cho SY, Jin DK

Abstract
Renpenning syndrome is a rare X-linked disorder characterized by mental retardation, leanness, microcephaly, facial dysmorphism, short stature, and small testes. This disease is caused by PQBP1 mutations. Herein, we present a literature review and describe the clinical and molecular findings in a Korean boy with Renpenning syndrome. A 23-month-old boy presented with mental retardation, narrow face, bulbous nose, and cardiac anomaly. Interestingly, targeted exome sequencing identified a novel mutation c.559delT (p.Tyr187llefs*8) in the PQBP1 gene, and he was diagnosed as having Renpenning syndrome. In line with previously reported studies, our case suggests that men with mental retardation, short stature, and microcephaly should include Renpenning syndrome as a differential diagnosis.

PMID: 30143497 [PubMed - in process]