The reversion variant (p.Arg90Leu) at the evolutionarily adaptive p.Arg90 site in CELA3B predisposes to chronic pancreatitis

ABSTRACTA gain-of-function missense variant in the CELA3B gene, p.Arg90Cys (c.268C>T), has recently been reported to cause pancreatitis in an extended pedigree. Herein, we sequenced the CELA3B gene in 644 genetically unexplained French chronic pancreatitis (CP) patients (all unrelated) and 566 controls. No predicted loss-of-function variants were identified. None of the six low frequency or common missense variants detected showed significant association with CP. Nor did the aggregate rare/very rare missense variants (n=14) show any significant association with CP. However, p.Arg90Leu (c.269G>T), which was found in 4 patients but no controls and affects the same amino acid as p.Arg90Cys, serves to revert p.Arg90 to the human elastase ancestral allele. Since p.Arg90Leu has previously been shown to exert a similar functional effect to p.Arg90Cys, our findings not only confirm the involvement of CELA3B in the etiology of CP but also pinpoint a new evolutionarily adaptive site in the human genome.

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Biological function polarity prediction of missense variants using machine learning

10.1101/2020.04.03.023440 ◽

2020 ◽

Author(s):

Adhideb Ghosh ◽

Alexander A. Navarini

Keyword(s):

Machine Learning ◽

Amino Acid ◽

Roc Curve ◽

Protein Level ◽

Biological Function ◽

Underlying Disease ◽

Loss Of Function ◽

Gain Of Function ◽

Missense Variants ◽

Bioinformatics Tools

AbstractFunctional interpretation is crucial when facing on average 20,000 missense variants per human exome, as the great majority are not associated with any underlying disease. In silico bioinformatics tools can predict the deleteriousness of variants or assess their functional impact by assigning scores, but they cannot predict whether the variant in question results in gain or loss of function at the protein level. Here, we show that machine learning can effectively predict this biological function polarity of missense variants. The new method adapts weighted gradient boosting machine approach on a set of damaging variants (1,288 loss of function and 218 gain of function variants) as annotated by the tools SIFT, PolyPhen2 and CADD. Area under the ROC curve of 0.85 illustrates high discriminative power of the classifier. Predictive performance of the classifier remains consistent against an independent set of damaging variants as highlighted by the area under the ROC curve of 0.83. This new approach may help to guide biological experiments on the clinical relevance of damaging genetic variants.Author summaryMissense variant occurs when a single genetic alteration in DNA takes place and as a result a new amino acid is translated into the protein. This amino acid change can inactivate the existing protein function causing loss-of-function or produce a new function causing gain-of-function. Therefore, it is very important to interpret these functional consequences of missense variants as they often turn out to be disease causing. Each individual’s genome sequence has thousands of missense variants, out of which very few are actually associated with any underlying disease. Various computational tools have been developed to predict whether missense variants are damaging or not, but none of them can actually predict whether the damaging missense variants cause gain-of-function or loss-of-function. We have developed a new ensemble classifier to predict this biological function polarity at the protein level. The classifier combines the prediction scores of three existing bioinformatics tools and applies machine learning to make effective predictions. We have validated our classifier against an independent data set to show its high predictive power and robustness. The predictions made by our machine learning tool can be used as indicators of biological function polarity, but with further evidence on pathogenicity.

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Novel mutation points to a hot spot in CDKN1C causing Silver–Russell syndrome

Clinical Epigenetics ◽

10.1186/s13148-020-00945-y ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Gerhard Binder ◽

Julian Ziegler ◽

Roland Schweizer ◽

Wisam Habhab ◽

Tobias B. Haack ◽

...

Keyword(s):

Amino Acid ◽

Adrenal Insufficiency ◽

Novel Mutation ◽

Hot Spot ◽

Missense Variant ◽

Single Family ◽

Loss Of Function ◽

Gain Of Function ◽

Functional Region ◽

Silver Russell Syndrome

Abstract Background Pathogenic CDKN1C gain-of-function variants on the maternal allele were initially reported as a cause of IMAGe syndrome characterized by intrauterine growth retardation, metaphyseal dysplasia, primary adrenal insufficiency and genital anomalies. Recently, a maternally inherited CDKN1C missense mutation (p.Arg279Leu) was identified in several members of a single family clinically diagnosed with Silver–Russell syndrome (SRS) but without adrenal insufficiency. Thereafter, two half siblings from UK with familial SRS were described who carried the same mutation. This specific amino acid change is located within a narrow functional region containing the mutations previously associated with IMAGe syndrome. Results Here, we describe a third familial case with maternally inherited SRS due to a missense variant affecting the same amino acid position 279 but leading to a different amino acid substitution (p. (Arg279Ser)). The two affected family members (mother and son) presented with the complete SRS phenotype (both Netchine–Harbison CSS score 5 of 6) but without body asymmetry or adrenal insufficiency. Conclusions In comparison with loss-of-function genomic IGF2 mutations, CDKN1C gain-of-function mutations are a less frequent cause of SRS and seem to affect a cluster of few amino acids.

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Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development

Genes ◽

10.3390/genes12040470 ◽

2021 ◽

Vol 12 (4) ◽

pp. 470

Author(s):

Jeremy W. Prokop ◽

Caleb P. Bupp ◽

Austin Frisch ◽

Stephanie M. Bilinovich ◽

Daniel B. Campbell ◽

...

Keyword(s):

Brain Development ◽

Neural Progenitor Cells ◽

Neurodevelopmental Disorder ◽

Fetal Brain ◽

Missense Variant ◽

Neural Progenitor ◽

Loss Of Function ◽

Gain Of Function ◽

Systematic Analysis ◽

Function Expression

Ornithine decarboxylase 1 (ODC1 gene) has been linked through gain-of-function variants to a rare disease featuring developmental delay, alopecia, macrocephaly, and structural brain anomalies. ODC1 has been linked to additional diseases like cancer, with growing evidence for neurological contributions to schizophrenia, mood disorders, anxiety, epilepsy, learning, and suicidal behavior. The evidence of ODC1 connection to neural disorders highlights the need for a systematic analysis of ODC1 genotype-to-phenotype associations. An analysis of variants from ClinVar, Geno2MP, TOPMed, gnomAD, and COSMIC revealed an intellectual disability and seizure connected loss-of-function variant, ODC G84R (rs138359527, NC_000002.12:g.10444500C > T). The missense variant is found in ~1% of South Asian individuals and results in 2.5-fold decrease in enzyme function. Expression quantitative trait loci (eQTLs) reveal multiple functionally annotated, non-coding variants regulating ODC1 that associate with psychiatric/neurological phenotypes. Further dissection of RNA-Seq during fetal brain development and within cerebral organoids showed an association of ODC1 expression with cell proliferation of neural progenitor cells, suggesting gain-of-function variants with neural over-proliferation and loss-of-function variants with neural depletion. The linkage from the expression data of ODC1 in early neural progenitor proliferation to phenotypes of neurodevelopmental delay and to the connection of polyamine metabolites in brain function establish ODC1 as a bona fide neurodevelopmental disorder gene.

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Identification and Characterization of Genes That Interact With lin-12 in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/147.4.1675 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1675-1695 ◽

Cited By ~ 2

Author(s):

Frans E Tax ◽

James H Thomas ◽

Edwin L Ferguson ◽

H Robert Horvitzt

Keyword(s):

Cell Fate ◽

Low Frequency ◽

Signal Transduction Pathway ◽

Temperature Shift ◽

Egg Laying ◽

Null Alleles ◽

Temperature Sensitive ◽

Loss Of Function ◽

Gain Of Function ◽

Suppressor Mutations

Abstract We identified and characterized 14 extragenic mutations that suppressed the dominant egg-laying defect of certain lin-12 gain-of-function mutations. These suppressors defined seven genes: sup-l7, lag-2, sel-4, sel-5, sel-6, sel-7 and sel-8. Mutations in six of the genes are recessive suppressors, whereas the two mutations that define the seventh gene, lag-2, are semi-dominant suppressors. These suppressor mutations were able to suppress other lin-12 gain-of-function mutations. The suppressor mutations arose at a very low frequency per gene, 10-50 times below the typical loss-of-function mutation frequency. The suppressor mutations in sup1 7 and lag-2 were shown to be rare non-null alleles, and we present evidence that null mutations in these two genes cause lethality. Temperature-shift studies for two suppressor genes, sup1 7and lag-2, suggest that both genes act at approximately the same time as lin-12in specifying a cell fate. Suppressor alleles of six of these genes enhanced a temperature-sensitive loss-of-function allele of glp-1, a gene related to lin-12 in structure and function. Our analysis of these suppressors suggests that the majority of these genes are part of a shared lin-12/glp-1 signal transduction pathway, or act to regulate the expression or stability of lin-12 and glp-1.

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CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants

Genetics in Medicine ◽

10.1038/s41436-020-01091-9 ◽

2021 ◽

Author(s):

Yuri A. Zarate ◽

Tomoko Uehara ◽

Kota Abe ◽

Masayuki Oginuma ◽

Sora Harako ◽

...

Keyword(s):

De Novo ◽

Loss Of Function ◽

Gain Of Function ◽

Related Disorder ◽

Missense Variants

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Ribosome Evolution and Structural Capacitance

10.20944/preprints201908.0266.v1 ◽

2019 ◽

Author(s):

Ashley M Buckle ◽

Malcolm Buckle

Keyword(s):

Amino Acid ◽

Genetic Code ◽

Protein Evolution ◽

Bioinformatic Analysis ◽

Amino Acid Usage ◽

Loss Of Function ◽

Gain Of Function ◽

Acceptor Stem ◽

Ribosome Evolution ◽

Disordered Regions

In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic ‘structural capacitance elements’. Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance – that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (DO) transition in previously disordered regions of proteins. Here we propose that the DO transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.

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A combined in silico, in vitro and clinical approach to characterise novel pathogenic missense variants in PRPF31 in retinitis pigmentosa

10.1101/480343 ◽

2018 ◽

Author(s):

Gabrielle Wheway ◽

Liliya Nazlamova ◽

Nervine Meshad ◽

Samantha Hunt ◽

Nicola Jackson ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

In Silico ◽

Autosomal Dominant ◽

Missense Variant ◽

Incomplete Penetrance ◽

Clinical Approach ◽

Loss Of Function ◽

Autosomal Dominant Retinitis Pigmentosa ◽

Missense Variants

AbstractAt least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localise to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood.In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T>A, p.Ile114Asn.This work demonstrates how in silico modelling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.

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Systematic analysis of PINK1 variants of unknown significance shows intact mitophagy function for most variants

npj Parkinson s Disease ◽

10.1038/s41531-021-00258-8 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Kai Yu Ma ◽

Michiel R. Fokkens ◽

Teus van Laar ◽

Dineke S. Verbeek

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Missense Variant ◽

Population Based ◽

Loss Of Function ◽

Systematic Analysis ◽

Missense Variants ◽

Variants Of Unknown Significance ◽

Disease Case ◽

Unknown Significance

AbstractPathogenic variants in PINK1 cause early-onset Parkinson’s disease. Although many PINK1 variants have been reported, the clinical significance is uncertain for the majority of them. To gain insights into the consequences of PINK1 missense variants in a systematic manner, we selected 50 PINK1 missense variants from patient- and population-wide databases and systematically classified them using Sherloc, a comprehensive framework for variant interpretation based on ACMG-AMP guidelines. We then performed functional experiments, including mitophagy and Parkin recruitment assays, to assess the downstream consequences of PINK1 variants. Analysis of PINK1 missense variants based on Sherloc showed that the patient databases over-annotate variants as likely pathogenic. Furthermore, our study shows that pathogenic PINK1 variants are most often linked to a loss-of-function for mitophagy and Parkin recruitment, while this is not observed for variants of unknown significance. In addition to the Sherloc framework, the added layer of evidence of our functional tests suggests a reclassification of 9/50 missense variants. In conclusion, we suggest the assessment of multiple layers of evidence, including functional data on top of available clinical and population-based data, to support the clinical classification of a variant and show that the presence of a missense variant in PINK1 in a Parkinson’s disease case does not automatically imply pathogenicity.

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De novo FZR1 loss-of-function variants cause developmental and epileptic encephalopathies including Myoclonic Atonic Epilepsy

10.1101/2021.06.12.21256778 ◽

2021 ◽

Author(s):

Sathiya N. Manivannan ◽

Jolien Roovers ◽

Noor Smal ◽

Candace T. Myers ◽

Dilsad Turkdogan ◽

...

Keyword(s):

De Novo ◽

Statistical Tests ◽

Essential Feature ◽

Missense Variant ◽

Anaphase Promoting Complex ◽

Loss Of Function ◽

Childhood Onset ◽

Epileptic Encephalopathies ◽

Missense Variants ◽

Generalized Epilepsy

FZR1, which encodes the Cdh1 subunit of the Anaphase Promoting Complex, plays an important role in neurodevelopment, both through the control of the cell cycle and through its multiple functions in post-mitotic neurons. In this study, the evaluation of 250 unrelated patients with developmental epileptic encephalopathies (DEE) and a connection on GeneMatcher led to the identification of three de novo missense variants in FZR1. Two variants led to the same amino acid change. All individuals had a DEE with childhood-onset generalized epilepsy, intellectual disability, mild ataxia, and normal head circumference. Two individuals were diagnosed with the DEE subtype Myoclonic Atonic Epilepsy (MAE). We provide gene burden testing using two independent statistical tests to support FZR1 association with DEE. Further, we provide functional evidence that the missense variants are loss-of-function (LOF) alleles using Drosophila neurodevelopment assays. Using three fly mutant alleles of the Drosophila homolog fzr and overexpression studies, we show that patient variants do not support proper neurodevelopment. Along with a recent report of a patient with neonatal-onset DEE with microcephaly who also carries a de novo FZR1 missense variant, our study consolidates the relationship between FZR1 and DEE, and expands the associated phenotype. We conclude that heterozygous LOF of FZR1 leads to DEE associated with a spectrum of neonatal to childhood-onset seizure types, developmental delay, and mild ataxia. Microcephaly can be present but is not an essential feature of FZR1-encephalopathy. In summary, our approach of targeted sequencing using novel gene candidates and functional testing in Drosophila will help solve undiagnosed MAE/DEE cases.

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Missense Variant of Endoplasmic Reticulum Region of WFS1 Gene Causes Autosomal Dominant Hearing Loss without Syndromic Phenotype

BioMed Research International ◽

10.1155/2021/6624744 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Jinying Li ◽

Hongen Xu ◽

Jianfeng Sun ◽

Yongan Tian ◽

Danhua Liu ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Hearing Loss ◽

Autosomal Dominant ◽

Low Frequency ◽

Missense Variant ◽

Normal Subjects ◽

Pathogenic Variant ◽

Chinese Family ◽

Missense Variants ◽

Wfs1 Gene

Objective. Genetic variants in the WFS1 gene can cause Wolfram syndrome (WS) or autosomal dominant nonsyndromic low-frequency hearing loss (HL). This study is aimed at investigating the molecular basis of HL in an affected Chinese family and the genotype-phenotype correlation of WFS1 variants. Methods. The clinical phenotype of the five-generation Chinese family was characterized using audiological examinations and pedigree analysis. Target exome sequencing of 129 known deafness genes and bioinformatics analysis were performed among six patients and four normal subjects to screen suspected pathogenic variants. We built a complete WFS1 protein model to assess the potential effects of the variant on protein structure. Results. A novel heterozygous pathogenic variant NM_006005.3 c.2020G>T (p.Gly674Trp) was identified in the WFS1 gene, located in the C-terminal domain of the wolframin protein. We further showed that HL-related WFS1 missense variants were mainly concentrated in the endoplasmic reticulum (ER) domain. In contrast, WS-related missense variants are randomly distributed throughout the protein. Conclusions. In this family, we identified a novel variant p.Gly674Trp of WFS1 as the primary pathogenic variant causing the low-frequency sensorineural HL, enriching the mutational spectrum of the WFS1 gene.

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