scholarly journals A Neurodevelopmental Disorder Caused by Mutations in the VPS51 Subunit of the GARP and EARP Complexes

2018 ◽  
Author(s):  
David C. Gershlick ◽  
Morié Ishida ◽  
Julie R. Jones ◽  
Allison Bellomo ◽  
Juan S. Bonifacino ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Genetic Locus ◽  
Neurodevelopmental Disorder ◽  
Failure To Thrive ◽  
The Other ◽  
Single Amino Acid ◽  
Global Developmental Delay ◽  
Compound Heterozygous ◽  
Acid Hydrolases ◽  
Gene Encoding

AbstractGARP and EARP are related heterotetrameric protein complexes that associate with the cytosolic face of the trans-Golgi network and recycling endosomes, respectively. At these locations, GARP and EARP function to promote the fusion of endosome-derived transport carriers with their corresponding compartments. GARP and EARP share three subunits, VPS51, VPS52 and VPS53, and each has an additional complex-specific subunit, VPS54 or VPS50, respectively. The role of these complexes in human physiology, however, remains poorly understood. By exome sequencing, we have identified compound heterozygous mutations in the gene encoding the shared GARP/EARP subunit VPS51 in a six-year-old patient with severe global developmental delay, microcephaly, hypotonia, epilepsy, cortical vision impairment, pontocerebellar abnormalities, failure to thrive, liver dysfunction, lower extremity edema and dysmorphic features. The mutation in one allele causes a frameshift that produces a longer but highly unstable protein that is degraded by the proteasome. In contrast, the other mutant allele produces a protein with a single amino-acid substitution that is stable but assembles less efficiently with the other GARP/EARP subunits. Consequently, skin fibroblasts from the patient have reduced levels of fully-assembled GARP and EARP complexes. Likely because of this deficiency, the patient’s fibroblasts display altered distribution of the cation-independent mannose 6-phosphate receptor, which normally sorts acid hydrolases to lysosomes. Furthermore, a fraction of the patient’s fibroblasts exhibit swelling of lysosomes. These findings thus identify a novel genetic locus for a neurodevelopmental disorder and highlight the critical importance of GARP/EARP function in cellular and organismal physiology.

scholarly journals NMIHBA results from hypomorphic PRUNE1 variants that lack short-chain exopolyphosphatase activity

2020 ◽  
Author(s):  
Harikiran Nistala ◽  
John Dronzek ◽  
Claudia Gonzaga-Jauregui ◽  
Shek Man Chim ◽  
Saathyaki Rajamani ◽  
...  
Keyword(s):  
Neurodegenerative Disorder ◽  
Neurodevelopmental Disorder ◽  
Cortical Atrophy ◽  
Global Developmental Delay ◽  
Compound Heterozygous ◽  
Genetic Ablation ◽  
Severe Intellectual Disability ◽  
Disease Biology ◽  
Variant Alleles ◽  
Clinical Description

Abstract Neurodevelopmental disorder with microcephaly, hypotonia and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G > A (p.Arg128Gln), c.520G > T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment.

EPG5 Variants with Modest Functional Impact Result in an Ameliorated and Primarily Neurological Phenotype in a 3.5-Year-Old Patient with Vici Syndrome

2019 ◽  
Vol 50 (04) ◽  
pp. 257-261 ◽  
Author(s):  
Megan S. Kane ◽  
Jia Zhao ◽  
Julie Muskett ◽  
Amelia Diplock ◽  
Siddharth Srivastava ◽  
...  
Keyword(s):  
Corpus Callosum ◽  
Failure To Thrive ◽  
Null Alleles ◽  
Neurological Involvement ◽  
Global Developmental Delay ◽  
Compound Heterozygous ◽  
Functional Impact ◽  
Messenger Ribonucleic Acid ◽  
Disease Spectrum ◽  
Neurological Phenotype

AbstractCongenital disorders of autophagy are multisystem disorders with significant neurological involvement. Ectopic p-granules protein 5 (EPG5)-associated Vici syndrome is a prototypical congenital disorder of autophagy and presents with the cardinal features of agenesis of the corpus callosum, cataracts, cardiomyopathy, immunodeficiency, and oculocutaneous hypopigmentation. The majority of EPG5 variants leading to Vici syndrome are null alleles with only a few missense variants published to date. Here we report a 3.5-year-old male with compound heterozygous EPG5 variants [NM_020964.2: c.772G > T/c.5943–9_5943–5del]. His clinical presentation deviates notably from classic Vici syndrome with a lack of hypopigmentation, cataracts, immunodeficiency, cardiomyopathy, or failure to thrive. Neurological manifestations within the known disease spectrum include early-onset global developmental delay, hypotonia, and postnatal microcephaly. Seizures, hearing loss, or optic nerve atrophy are absent, however. Magnetic resonance imaging demonstrates a thin but fully formed corpus callosum. Based on the ameliorated and primarily neurological phenotype, we hypothesized that the functional impact of the EPG5 variants present would be milder with a higher amount of residual EPG5 expression. Analyses of EPG5 messenger ribonucleic acid (mRNA) in the patient and his parents were performed to examine expression level and splicing; mRNA from a healthy control and a patient with classic Vici syndrome was also included. Aberrant splicing due to the intronic mutation was detected, but no loss of expression. In contrast, we observed a 50% reduction in mRNA expression in classic Vici syndrome patient fibroblasts. These results support a model of disease severity, which correlates to the dosage of EPG5 expression.

117 Improved Growth Performance in the F1 Heterozygous Generation of an SSTR2 Knockout Model in Swine

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 36-36
Author(s):  
R Blythe Schultz ◽  
Malavika K Adur ◽  
Yunsheng Li ◽  
Zoe E Kiefer ◽  
Nicholas K Gabler ◽  
...  
Keyword(s):  
Growth Performance ◽  
Anterior Pituitary ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
The Other ◽  
Single Amino Acid ◽  
Compound Heterozygous ◽  
Production Traits ◽  
State University ◽  
Negative Effect

Abstract Targeted genetic alteration provides opportunities for rapid genetic improvement in resilience, welfare and production traits. Somatostatin (SST) acts via negative feedback to regulate growth hormone (GH) activity by antagonizing GH releasing hormone via SST receptors (SSTR) located in the anterior pituitary. Our objective was to reduce the negative effect of SST in the anterior pituitary on protein accretion by reducing the number of functional copies of SSTR2 using the CRISPR/Cas9 system. We hypothesized that a reduction or elimination of SSTR2 would lead to improved growth performance. To test this hypothesis, three commercial gilts were bred with semen from a founder boar in a compound heterozygous state at the SSTR2 locus with a 1bp deletion in one allele resulting in a premature stop codon and a 3bp deletion in the other allele resulting in the loss of a single amino acid predicted to remain functional after translation. Three litters of F1 offspring were produced (n = 46) and all piglets were confirmed to be heterozygous at the SSTR2 locus with one wild type allele and the other possessing either the 1bp deletion (n = 22) or the 3bp (n = 2 4) deletion. No differences (P > 0.43; n=46) in body weight (1.27±0.03 kg) across comparisons were observed at birth. At weaning (n = 36), males (6.19±0.20 kg) were heavier (P = 0.007) than females (5.41±0.19 kg), and piglets possessing a 1bp deletion (6.00±0.20 kg) were numerically heavier (P = 0.14) than 3bp deletion pigs (5.59±0.18 kg). This observation was more pronounced in males at weaning, where the males with the 1bp deletion were 13% heavier (P = 0.058) than those with the 3bp deletion. These data suggest that altering SSTR2 may be a viable genetic advancement strategy to improve growth performance in pigs. This project was supported by the Lloyd L. Anderson Professorship in Physiology at Iowa State University.

scholarly journals Novel Compound Heterozygous Variants in TBCD Gene Associated with Infantile Neurodegenerative Encephalopathy

Children ◽  
2021 ◽  
Vol 8 (12) ◽  
pp. 1140
Author(s):  
Chih-Ling Chen ◽  
Chien-Nan Lee ◽  
Yin-Hsiu Chien ◽  
Wuh-Liang Hwu ◽  
Tung-Ming Chang ◽  
...  
Keyword(s):  
Early Onset ◽  
Neurodegenerative Disorder ◽  
Failure To Thrive ◽  
Compound Heterozygous ◽  
Gene Encoding ◽  
Pathogenic Variants ◽  
Compound Heterozygous Variants ◽  
Relationship Of ◽  
Compound Heterozygotes ◽  
Insight Into

Mutations in tubulin-specific chaperon D (TBCD), the gene encoding one of the co-chaperons required for the assembly and disassembly of the α/β-tubulin heterodimers, have been reported to cause perturbed microtubule dynamics, resulting in debilitating early-onset progressive neurodegenerative disorder. Here, we identified two novel TBCD variants, c.1340C>T (p.Ala447Val), and c.817+2T>C, presented as compound heterozygotes in two affected siblings born to unaffected carrier parents. Clinical features included early-onset neurodegeneration, failure to thrive, respiratory failure, hypotonia, muscle weakness and atrophy and seizures. We established the genotype–phenotype relationship of these TBCD pathogenic variants and provided insight into the protein structural alteration that may contribute to this chaperone-associated tubulinopathy.

scholarly journals Functional modeling of NMIHBA-causing PRUNE1 variants reveals a requirement for its exopolyphosphatase activity

2020 ◽  
Author(s):  
Harikiran Nistala ◽  
John Dronzek ◽  
Claudia Gonzaga-Jauregui ◽  
Shek Man Chim ◽  
Saathyaki Rajamani ◽  
...  
Keyword(s):  
Neurodegenerative Disorder ◽  
Neurodevelopmental Disorder ◽  
Cortical Atrophy ◽  
Global Developmental Delay ◽  
Compound Heterozygous ◽  
Genetic Ablation ◽  
Severe Intellectual Disability ◽  
Disease Biology ◽  
Variant Alleles ◽  
Clinical Description

AbstractNeurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G>A (p.Arg128Gln), c.520G>T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment.

scholarly journals Shukla-Vernon Syndrome: A Second Family with a Novel Variant in the BCORL1 Gene

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 452
Author(s):  
Babylakshmi Muthusamy ◽  
Anikha Bellad ◽  
Satish Chandra Girimaji ◽  
Akhilesh Pandey
Keyword(s):  
Intellectual Disability ◽  
Developmental Delay ◽  
Protein Complexes ◽  
Neurodevelopmental Disorder ◽  
Missense Variant ◽  
Global Developmental Delay ◽  
Dysmorphic Features ◽  
Pathogenic Variants ◽  
Behavioral Abnormalities ◽  
Novel Variant

Shukla-Vernon syndrome (SHUVER) is an extremely rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, behavioral anomalies, and dysmorphic features. Pathogenic variants in the BCORL1 gene have been identified as the molecular cause for this disorder. The BCORL1 gene encodes for BCL-6 corepressor-like protein 1, a transcriptional corepressor that is an integral component of protein complexes involved in transcription repression. In this study, we report an Indian family with two male siblings with features of Shukla-Vernon syndrome. The patients exhibited global developmental delay, intellectual disability, kyphosis, seizures, and dysmorphic features including bushy prominent eyebrows with synophrys, sharp beaked prominent nose, protuberant lower jaw, squint, and hypoplastic ears with fused ear lobes. No behavioral abnormalities were observed. Whole exome sequencing revealed a novel potentially pathogenic arginine to cysteine substitution (p.Arg1265Cys) in the BCORL1 protein. This is the second report of Shukla-Vernon syndrome with a novel missense variant in the BCORL1 gene. Our study confirms and expands the phenotypes and genotypes described previously for this syndrome and should aid in diagnosis and genetic counselling of patients and their families.

scholarly journals A Single Point Mutation, Asn16→Lys, Dictates the Temperature-Sensitivity of the Reovirus tsG453 Mutant

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 289
Author(s):  
Kathleen K. M. Glover ◽  
Danica M. Sutherland ◽  
Terence S. Dermody ◽  
Kevin M. Coombs
Keyword(s):  
Amino Acid ◽  
Temperature Sensitivity ◽  
Reverse Genetics ◽  
Core Protein ◽  
Single Point ◽  
Single Amino Acid ◽  
Single Point Mutation ◽  
Temperature Sensitive ◽  
Amino Acid Substitutions ◽  
Gene Encoding

Studies of conditionally lethal mutants can help delineate the structure-function relationships of biomolecules. Temperature-sensitive (ts) mammalian reovirus (MRV) mutants were isolated and characterized many years ago. Two of the most well-defined MRV ts mutants are tsC447, which contains mutations in the S2 gene encoding viral core protein σ2, and tsG453, which contains mutations in the S4 gene encoding major outer-capsid protein σ3. Because many MRV ts mutants, including both tsC447 and tsG453, encode multiple amino acid substitutions, the specific amino acid substitutions responsible for the ts phenotype are unknown. We used reverse genetics to recover recombinant reoviruses containing the single amino acid polymorphisms present in ts mutants tsC447 and tsG453 and assessed the recombinant viruses for temperature-sensitivity by efficiency-of-plating assays. Of the three amino acid substitutions in the tsG453 S4 gene, Asn16-Lys was solely responsible for the tsG453ts phenotype. Additionally, the mutant tsC447 Ala188-Val mutation did not induce a temperature-sensitive phenotype. This study is the first to employ reverse genetics to identify the dominant amino acid substitutions responsible for the tsC447 and tsG453 mutations and relate these substitutions to respective phenotypes. Further studies of other MRV ts mutants are warranted to define the sequence polymorphisms responsible for temperature sensitivity.

scholarly journals Unusual phenotypes in patients with a pathogenic germline variant in DICER1

2021 ◽  
Author(s):  
Kateryna Venger ◽  
Miriam Elbracht ◽  
Julia Carlens ◽  
Peter Deutz ◽  
Felix Zeppernick ◽  
...  
Keyword(s):  
Wilms Tumor ◽  
Pleuropulmonary Blastoma ◽  
Global Developmental Delay ◽  
Facial Dysmorphism ◽  
Compound Heterozygous ◽  
Incomplete Penetrance ◽  
Developmental Abnormalities ◽  
Lung Cysts ◽  
Developmental Features ◽  
Skeletal Findings

AbstractPathogenic germline DICER1 variants are associated with pleuropulmonary blastoma, multinodular goiter, embryonal rhabdomyosarcoma and other tumour types, while mosaic missense DICER1 variants in the RNase IIIb domain are linked to cause GLOW (global developmental delay, lung cysts, overgrowth, and Wilms’ tumor) syndrome. Here, we report four families with germline DICER1 pathogenic variants in which one member in each family had a more complex phenotype, including skeletal findings, facial dysmorphism and developmental abnormalities. The developmental features occur with a variable expressivity and incomplete penetrance as also described for the neoplastic and dysplastic lesions associated with DICER1 variants. Whole exome sequencing (WES) was performed on all four cases and revealed no further pathogenic or likely pathogenic dominant, homozygous or compound heterozygous variants in three of them. Notably, a frameshift variant in ARID1B was detected in one patient explaining part of her phenotype. This series of patients shows that pathogenic DICER1 variants may be associated with a broader phenotypic spectrum than initially assumed, including predisposition to different tumours, skeletal findings, dysmorphism and developmental abnormalities, but genetic work up in syndromic patients should be comprehensive in order not to miss additional underlying /modifying causes.

scholarly journals Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1053
Author(s):  
Jasleen Dhaliwal ◽  
Ying Qiao ◽  
Kristina Calli ◽  
Sally Martell ◽  
Simone Race ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Rare Variants ◽  
Neurodevelopmental Disorder ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Compound Heterozygous ◽  
Variable Effect ◽  
Gabaergic Neurotransmission ◽  
High Heritability ◽  
Compound Heterozygous Variants

Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in children and shows high heritability. However, how inherited variants contribute to ASD in multiplex families remains unclear. Using whole-genome sequencing (WGS) in a family with three affected children, we identified multiple inherited DNA variants in ASD-associated genes and pathways (RELN, SHANK2, DLG1, SCN10A, KMT2C and ASH1L). All are shared among the three children, except ASH1L, which is only present in the most severely affected child. The compound heterozygous variants in RELN, and the maternally inherited variant in SHANK2, are considered to be major risk factors for ASD in this family. Both genes are involved in neuron activities, including synaptic functions and the GABAergic neurotransmission system, which are highly associated with ASD pathogenesis. DLG1 is also involved in synapse functions, and KMT2C and ASH1L are involved in chromatin organization. Our data suggest that multiple inherited rare variants, each with a subthreshold and/or variable effect, may converge to certain pathways and contribute quantitatively and additively, or alternatively act via a 2nd-hit or multiple-hits to render pathogenicity of ASD in this family. Additionally, this multiple-hits model further supports the quantitative trait hypothesis of a complex genetic, multifactorial etiology for the development of ASDs.

scholarly journals Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ilaria Mannucci ◽  
Nghi D. P. Dang ◽  
Hannes Huber ◽  
Jaclyn B. Murry ◽  
Jeff Abramson ◽  
...  
Keyword(s):  
De Novo ◽  
Clinical Course ◽  
Neurodevelopmental Disorder ◽  
Global Developmental Delay ◽  
Helicase Activity ◽  
Speech Impairment ◽  
Human Phenotype ◽  
Missense Variants ◽  
The Impact ◽  
Global Translation

Abstract Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories.

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